I think it's easily the Gambinos. Most of the big families had leaders "touched" at one point or another, but the Gambinos had multiple bosses or underbosses clipped.

Colombos: Joe Colombo, a boss.

Bonnanos: Galante, the 3 Captains(they were not leadership technically, but high ranking)

Genovese: Zeccardi, either a boss or a front boss, depending on who you ask

Chicago: Giancana, and maybe Nitti if you want to count him in, both acting/front bosses, depending on who you ask

Gambinos: Mangano, Anastasia, Castellano, DeCicco

I'm probably leaving out a bunch of high ranking captains but it's clear to me the Gambinos come out on top, or at the bottom, depending on how you look at it.