Odin, Seth, Galactus, Tyrant, Beyonder, Abraxas, Anti-Monitor, Mxyzptlk, Bat-Mite, Eternity (well if he hasn't he obviously could, since all the galaxies in the universe are part of his own body), Living Tribunal destroyed universes I think, and was in one scan stated to have "power coursing through his fingers strong enough to instantly vaporize galaxies". Lucifer Morningstar destroyed a dimension I think, so did Doctor Strange, Surtur did I think, the Amalgam Brothers were destroying universes, Imperiex threatened to destroy the universe and almost did by releasing the power of the Big Bang, in one comic Darkseid being removed from the timeline caused all of time to start unwravelling, Mephisto destroyed galaxies in his fight with Galactus I think, Parallax remade the universe, etc.
I know the Living Tribunal has the power to do so, of course all of the retcon beings like the 'Brothers', Beyonder, and the Molecue Man. There was a being named Zom who had vast power