Are you really comparing the active harbor, with its tankers, ferrys, coast guard, private boats, barges, debris, choppy water, boat wakes, pollution, and security concerns to the calm that is the charles river basin?
As for pleasure bay, have you looked at the charles during the nice weather? It's packed with boats. There is no way they would all fit there, and even if they could, the boathouses would take up the entire circumference.
We are really, really, REALLY lucky to have the Charles basin. I would actually argue for recreating the south bay in hope it might create a twin on the south side of the city.