This is a very hard question to answer.
You have the following list of Yankees that were around well before Jeter.
You have Mantle, DiMaggio, Gehrig, Ford, Rizzutto, Ruth, some can even say Mattingly was the best.
I guess it would all depend on when you were alive and who you saw.
If you go by statistics only, Babe Ruth would be, but as a leader, you have three that come to mind.
Mattingly, Jeter and Munson were by far in my lifetime the leaders of the Yankees. O'Neal would have been in there if he was home grown tallent. He was from the Reds so I can't add him.
Any way you look at it, you would have a valid argument for Jeter.. I am glad I do not have to make a choice.