I guess I'll just copypasta a comment I made a long time ago, as it's completely relevant to this situation.

Both were fantastic Assassins, who impacted the world in ways that, ironically, the world will never even know about. But look at the personalities of each one. Altair, later in the game, because wizened. But during the majority of the game, he was a selfish, arrogant, headstrong, prideful ass.
Ezio was arrogant at times as well, and he did things motivated out of revenge instead of the greater good, but he was always more careful. He was more prone to plan things, to go in carefully, to take out his targets with as little collateral damage as possible. In my humble opinion, Ezio will always trump Altair. I feel he was not only a superior Assassin, but a superior person as well.
I also feel Ezio was just all around more skilled. He was the leader of the largest organization in both Rome and Constantinople at the time; the Assassins Guild. I think that being that leader, and earning his power and status taught him a lot of things. Things that Altair didn't have the opportunity to learn as early as Ezio did. Again, both were fantastic Assassins.
TL;DR I think Ezio is better because reasons.