To replace the ferry terminal that they built during the Big Dig and then promptly tore up. Great planning...
It's probably also worth noting that the Charlestown Bridge is a real limiting factor here. You can't get the Navy Yard Ferry, or the Hingham/Hull, Salem, Lynn Seasonal, etc. under there. Best you can hope for is the Cultural Connector and the Water Taxi. I've never seen the numbers on those, but I'd assume they aren't great. But for only a couple hundred thousand? Whatever, that's not a huge outlay.