You wish to know who would win at their peak. Well, I am not familiar with Darkseid's peak. However, Thanos' peak probably occured when he obtained the Heart of the Universe. Wikipedia has this to say:
The artifact makes Thanos a part of everything, and able to absorb the entire universe - even the cosmic entities Eternity, Infinity and the Living Tribunal. After literally ending the universe, Adam Warlock (who exists outside the space-time continuum) explains to Thanos that the constant resurrection of beings has caused an impurity in the old universe that only he can fix. Thanos then restarts the universe and sacrifices himself to fix the flaw.
Wikipedia also concisely states the artifact's power with the following:
The Heart of the Universe is the most powerful object in the entire Marvel Comics Universe, above that of the Cosmic cubes, the Great Powers of the Universe, the Infinity Gauntlet, and even the Living Tribunal itself.
Of course, Thanos turned up alive nonetheless, and it is unclear whether he or anyone else still has access to the artifact. Recently, it has been suggested by writer Keith Giffen that Thanos may become the new Death. If so, this also effects the outcome of a fight with Darkseid, as Death is capable of keeping the soul outside of her realm and hence, the soul continuously restructures matter to re-form a body.