There's already a ferry system in the bay to points where it's feasible to to put docks. However, much of the bay is less than ten feet deep, with gentle slopes, which make ferries to other points, especially in the south bay, difficult.

Boats, as the saying goes, are holes in the water that you throw money into.

It's generally better to invest up front on a bridge or tunnel. You wind up with a much, much lower cost for daily operations...