The Marvel Universe has plenty of gods and deities that can overtake even the strongest of anime protagonists. Anime likewise has plenty of gods and goddesses that can rival them.
Most godlike beings have the same innate abilities: cause and effect, time and space, planetary if not universal, and multiversal destruction; the list goes on into infinity. This list will detail the strongest gods in the Marvel Universe and gods within anime that can rival them.
Note: This list will contain spoilers for events related to Marvel comics and various anime. The Marvel universe is far too vast, and this list will have abridged histories.
Note 2: As always, this is only the author's opinion. Honorable mentions are also included.
The five strongest Marvel gods
Eternity is the Marvel Universe incarnate. Essentially, the representative being of all that is and will be in the universe, all the planets and beings live within Eternity. He is the beginning and the end of the Marvel Universe and brother to Inifinity, who represents infinite growth.
Though Eternity, Infinity, and Oblivion further down this list represent concepts, they are by no means weak. Eternity is the personification of time, and as such, his powerset includes night omnipotence, unlimited power to manipulate time, energy, matter, space, magic, or reality, and restoring planets that are destroyed.
2) The One Above All
The One Above All sees through many eyes, builds with many hands, and is, in general, the supreme ruler of the Marvel Multiverse and the ultimate godly and cosmic source of good and love in the Marvel universe. Rarely intervening unless necessary, the One Above All is split between this form and its demonic counterforce entity, the One Below All.
Like the One Above All, they are omnipotent, compassionate, omnipresent, and omnipotent, allowing it to see all, hear it all, and come down to aid those who need the air in times of genuine crisis. Like the One Below All, it's the opposite, as it destroys and consumes in near mindless hunger to destroy life and make way for a new universe to spawn. It is above even The Living Tribunal's area of expertise.
3) The Beyonder
I am from beyond! Slay your enemies and all you desire shall be yours! Nothing you dream of is impossible for me to accomplish!
The Beyonder proves this statement to be no mere boast in the crossover. He transported various heroes, including The Hulk, Spider-Man, members of the Fantastic Four, X-Men, and Avengers, alongside many villains like Doctor Doom, Doctor Octopus, Ultron, and Galactus to a massive patchwork planet called Battleworld and had them battle for his amusement.
The Beyonder's powers have generally fluctuated due to Marvel's penchant for retcons. To simply these powers, The Beyonder is indeed a reality-warping god. He conquered Earth with a thought, created Battleworld with pieces from hundreds of planets, can assimilate knowledge throughout the multiverse, and can easily change matter and reality at will.
He was at one time only surpassed by the One Above All.
4) The Living Tribunal
The Living Tribunal, aka the Living Trinity, is meant to be a Marvel multi-versal safeguard. They are intended to protect the multiverse from an imbalance of mystical forces, preventing Good or Evil from overwhelming the multiverse. It also has three sides to its personality: the front face of equity, the hooded right face of necessity, and the left of revenge. All three must agree before intervention.
The Living Tribunal is powerful enough to obliterate planets, turn stars into supernovas with a mere flick, and was powerful enough to nullify the Infinity Gems. The Tribunal was powerful enough to rival and overcome Infinity and Eternity and sealed off an alternate Earth to prevent devastation from spreading outward.
The progenitor of Death and representative of non-existence. Oblivion predates the Marvel Multiverse and is a counter-force to the expanding universe. Oblivion represents the primordial darkness that existed before creation and the ultimate destruction of the cosmos. It sees fellow cosmic entities like Eternity and Infinity as siblings and rivals.
The only thing about Oblivion is that, while its power is supreme in and of itself, it relies on Avatars to fight in the mortal plane. Knull, for instance, was born in that void, The Chaos King was an avatar, but the one that lasted the longest was Maelstrom. He was given powers over darkness and entropy but was stopped by the equally powerful avatar of Infinity Quasar.
The Pheonix Force
The Pheonix Force is a cosmic entity capable of utterly destroying almost anything in its path as it goes to different hosts, trying to find someone to enact its will throughout the Marvel Universe. The fact that it's been defeated multiple times, generally by the X-Men, and sealed away precludes it from this list.
The God of Symbiotes/The Symbiote King would've made it on this list were it not for being outmatched by the ever more powerful cosmic beings above. Knull doesn't quite get up to cosmic levels despite having control over an entire planet as the others do.
Odin is the same story as Knull, only with a different tune. Odin is already a god, the All-Father of Asgard. But even with such power that he wields, he's still nothing compared to the sheer scale and might the more cosmic beings weild. Plus, he's usually in Odinsleep when audiences see him.
The five strongest Anime gods
1) Grand Zeno - Dragon Ball Super
The Grand Zeno of the shonen anime Dragon Ball Super can certainly give more than a few Marvel entries a run for their money. Zeno has used entire universes as playthings and wiped out absolute realities. It's worse when there are two of them, as even the Gods of Destruction fear them in the anime.
The drawback, of course, to Zeno, is the childlike mindset they possess. The two are more interested in seeing a good fight but won't hesitate to erase what they see as a threat when Infinite Zamasu takes over Trunk's reality. The Tournament of Power also showed the ability to erase entire multiverses/universes lost, no matter how powerful they were.
2) Haruhi Suzumiya - The Melancholy of Haruhi Suzumiya
Marvel's The Beyonder may be able to create whatever he wishes, but Haruhi Suzumiya has him beat. Long story short, Haruhi is God in human form, and her emotional state dictates what reality is in the anime The Melancholy of Haruhi Suzumiya. Every subconscious wish of hers immediately springs into being: whether it's ESP, aliens, or time loops, as seen in Endless Eight.
The SOS Brigade has to keep Haruhi's emotions in check; otherwise, she creates closed-off spaces of reality in which giant monsters called Celestials rampage. She also created alternate realities, changed the weather, made film events a fact, and changed her class seating arrangements.
3) Truth - Fullmetal Alchemist Brotherhood
The Truth from the anime Fullmetal Alchemist Brotherhood/The Manga is hard to explain adequately. Being as simplistic as possible, Truth enforces the Rules of Equivalent Exchange across all planets in the universe. Think of it as the gatekeeper of God's domain, punishing any would-be alchemist that tries to play God.
The Homunculus leader Father learned this hard, as trying to rule the world using Truth's power backfired on him hard. His body deteriorated rapidly, his strength left him, and Truth sent Father to eternal torment in the Gate of Truth. Truth did, however, applaud Edward Elric's final understanding of the Equivalent Exchange and allowed him to pass as Edward gave up alchemy and his Gate.
4) Arceus - Pokémon
The creator of all Pokémon life and the universe in both games and the anime, Arceus was the progenitor of the Sinnoh, Hisui, and Ransei regions, alongside the creation trio of Palkia, Giratina, Dialga, and the lake guardians Uxie, Mesprit, and Azelf. To say that means Arceus is necessary is an understatement and a match for Marvel's the Beyonder.
Arceus' powers eclipse its creations. It manipulates time and space at will and controls several dimensions. It can swap between all the known Pokémon types on the fly via plates. Judgment's ultimate move is a large beam of light followed by bright pink meteorites that devastate the land and world, as seen in the anime movie Pokémon: Arceus and the Jewel of Life when it destroyed Minchina Town and threatened the world.
5) The Anti-Spiral - Tengen Toppa Gurren Lagann.
If not the Living Tribunal, one that could probably rival Eternity is the Anti-Spiral from the mecha anime Gurren Lagann. A manifestation of the will and mind of the Anti-Spiral race, the Anti-Spiral is obsessed with destroying all life forms. So, he and Marvel's Oblivion would get along swimmingly, if nothing else.
The Anti-Spiral's whole MO is that he wants to stop Spiral Nemesis, an apocalyptic level event that would spell doom for the multiverse. He does this by trying to destroy the Earth, the universe, and all life using such godlike abilities as throwing planets around, manipulating probability, reality-warping, and creating a literal Big Bang as an attack. Though he comes at the end of the anime, he's a god to be feared.
Deus Ex Machina - Mirai Nikki/Future Diaries
Dues Ex Machina is the creator of Future Diaries from the anime of the same name. His goal throughout the anime is to try to gain a host that can contain him, so his death doesn't destroy the universe. He is the judge of the Survival Game, can rewind and leap back through time, have the powers of causality, and create parallel worlds. He's also tied to all creation, as his death will destroy the universe.
He narrowly lost out on the list due to not being omnipotent and omniscient, and he's oblivious to the existence of one of the alternate worlds.
Madoka Kaname - Puella Magi Madoka Magica
Madoka only became a goddess at the tail end of the anime Madoka Magica; thus, she's officially off the list for that alone. That said, her power and abilities were enough to rewrite the laws of reality so that Kyuby's system is ultimately toppled and magical girls can rest in peace following death and not become witches.
Ryuk - Death Note
Despite essentially being death incarnate as a shinigami, one of many in anime, Ryuk mostly sticks to his function of killing via the Death Note. After all, he only gave it to Light Yagami because he was bored. His presence as a background threat likewise precludes him from being on the list, as we don't know his full capabilities. Elsewise, they're never shown in the anime proper.