There's been a lot of talk of reviving ferries in Boston, and NYC has gone full steam ahead on ferries in the East River. So here's a thought:
Last year I visited Bangkok, where ferries shuttle tourists and locals up and down the Chao Phraya River. Theses aren't your typical ferries--they are small and fast, with the crew incredibly adept at docking, loading/off-loading passengers, and pushing off again quickly and efficiently. Docks are minimal, dwell times are minimal, and headways are around 10 minutes. This is truly a form of rapid transit on water.
Why can't Boston replicate this kind of ferry system? Rather than a bunch of point-to-point routes (Charlestown-Long Wharf, proposed North Station-Fan Pier, etc.) that are constrained in the ridership they can attract, why not a linear "Aqua Line" that links the entire inner harbor together:
Assembly Square-Chelsea Waterfront-Central Square-Charlestown Navy Yard-N. Station-Long Wharf-S. Station-Fan Pier-Design Center/Marine Industrial Park-Castle Island
The key to this is speed. None of these big, lumbering ferries that take forever to dock, load, and go. Smaller, faster boats, max 15 minute headways, and Charlie Card 2.0 integration would make this a hit and take full advantage of the harbor while being completely unique among US transit systems.