A ferry option would be terrific.
It's actually doable at all the sites still on the board. GAL is relatively close to the Harlem River, although its not clear how easy it would be to put a dock there that would shuttle people over the train line and street that hug the river. Same is true of the other S. Bronx site that is just down river a bit and right on the water.
In Willets, there is already a marina on Flushing Bay that is fairly close to Willets Point, and it should be easy to put something new in even closer. It might also be possible to put something on the Flushing River, although I don't know about depth and whether it would be considered okay to build along the shore or even whether you could get people over or under the Van Wyck.
Of course, nothing will be as good for this as the Fresh Direct site, which is right on Newtown Creek and therefore a really easy trip from a huge portion of the city.