Frank Costello was a great businessman, bot I'm not sure if he was in fact also a good crime boss. You need more than brains for that.

Joe Bonanno sat on the top for over 30 years, that says something.. For the rest, the obvious ones, Luciano, Accardo, Gambino, Gigante..

I won't name Santo Trafficate. While he could very well have been a capable leader, he was never tested to run a very large criminal organization like the ones in New York or Chicago.