That's an interesting question. I suppose it depends on your definition of "best".
Altair was a duty-driven killer. He strayed from the Creed but soon re-embraced it and is truly the reason the order of Assassins spread outside of the Middle-East. Without him, none of the other Assassins would probably exist. Although he was arrogant, I would say that he was perhaps the must dutiful and efficiently silent-killer.
Ezio was a revenge-driven individual. He accomplished some amazing tasks and is truly the only reason the Assassin's Brotherhood was able to be re-invented and to survive past the Renaissance. As a warrior, I would say that Ezio was perhaps the best fighter and the assassin with one of the most impressive careers.
Connor was a justice-driven soldier, fighting for his people. His actions also aided in the rebirth of the diminished Assassin's order during the American Revolution. He was the best representation of an underdog rising and changing the order of his region.
All of this to say that it's hard to choose who would be the best Assassin. They had different qualities which made them individually superior. However, out of character preference, I might choose Ezio. However as for being an Assassin, I suppose that Altair would probably be considered the best of them all, but again, this is just a personal preference.