Some good guesses guys. But I think Don Pep is closest to the actual mark for NY waterfront mob domination. It's a tricky answer because depending upon what borough or section of the NYC docks we're speaking of different crews were the strongest. For instance;

On the Lower Eastside (and Lower Westside docks) the Vito Genovese Family's rule was almost 100% in control. The Upper Westside docks were actually under the dominion of the old "Arsenal Mob" which was a predominantly Irish mob of hoodlums. But they also worked in tandem along those docks with the Genovese mob so there's that.

Also having a presence along the LES docks were such Bonanno men as (Al Embarrato, Frank and Angelo Presenzano, etc).

On the Brooklyn docks without a doubt the old Anastasia/Gambino Family generally ruled the roost (think Tough Tony Anastasio, Tony Scotto, and Tony Anastasio). But on the South Brooklyn docks by the Gowanus Bay the Profaci/Colombo Family also had a strong presence (Tommy DiBella, Frank LoFaro, Harry Fontana). So Anastasia/Gambino shared power with Profaci/Colombo. For that matter several key members of the DeCavalcante Family's Brooklyn crew were also active there (Umberto and Angelo Gallo, and Jimmy Rotondo who was a top ILA official).

On the Staten Island docks it was all Anastasia/Gambino who ruled through a capo named Alex DeBrizzi ran a dock union with his nephews.

So here's my take on it;

1) Genovese was strongest in Manhattan
2) Gambino was strongest in Brooklyn & SI.
Don Pep's assessment of a wide margin in-between is correct I feel
3) Colombo and Bonanno tie for 3rd place (although I give the edge to Colombo who had a heavier presence I feel)
4) DeCavalcante
5) Lucchese had virtually zero presence whatsoever along any docks. It wasn't their neck of the woods.

PS: [on NJ's docks it's Genovese because of sheer numbers, but the DeCavalcante Family also held major sway through a dock union local they've controlled forever.]