Evidently, the NY harbor was split up between the control of two families...

The Gambinos, and the Genovese.

The Anastasia family controlled the Brooklyn waterfront, and the Luciano Family controlled the Manhattan waterfront. Hope I didn't get that reversed.

It makes sense that those were the two biggest and most important families whose bosses have been called boss of bosses historically.

The biggest boss supervised the biggest cash crop (heroin) for the Commission. It must have been shared with the Commission to keep the peace and because each Boss must have made an investment of their own in the outsourced heroin trade the Sicilians helped them move.