(Review of the marina's houseboat rentals, not the marina or boat repair service.) For houseboat rentals, Boston Bay Marina turned out to be an awesome alternative to a hotel. We rented 2 of their houseboats, Andromeda and Lyra, for a college graduation weekend. (There's also at least one much bigger houseboat and others of similar size.) Each sleeps six: two in a stateroom, two in the loft over the stateroom ceiling (uh, deck I think it's called), two on a pull-out sofa. Two decks outside, upper and lower, with a great view of Boston's working harbor (Chelsea River, Mystic River Bridge). The staff was friendly and fixed a couple minor issues quickly (BBQ grill wouldn't light initially). Our houseboats had one bathroom (toilet, sink, shower) but there are also marina showers for transient boaters who also use the marina. There's electric heat and a pair of air conditioners, TV, iPod dock/speakers, and a refrigerator-sink-electric stove galley (kitchen).
East Boston is a rapidly gentrifying part of Boston with condo and townhouse construction coming. You can get to Boston by walking a block, taking the bus 10 minutes to the T (subway) station, and then it's quickly into Boston. The rental includes free water taxi shuttle into Boston a couple times a day plus you can reserve a time slot in advance. The marina also rents pier space to boat owners, transient boats,and has a couple long-term tenants, all giving it a nice charming flavor. You'd expect to hear "Margaritaville" break out at any moment.
Our review rating is 4.5 stars rounded up. The boats are clean and work well but you see a couple signs of wear, as you'd expect of boats not maintained by dot-com millionaires. You'll hear some road noise from the McArdle bridge grating. Wifi is free but would benefit from one more repeater. Some renters may (may not will) wish they were renting on fancier Rowe's Wharf but it's likely you'd be paying twice as much. The marina is behind an auto body shop but a) this is the cleanest auto body shop you'll ever see (no wrecks in sight) and b) that also means secure, free parking.
Here can you get up early on a Sunday morning to see a glass-smooth harbor and two tugs threading a giant ocean-going ship through Boston Harbor. That was an awesome way to have the day's first cup of coffee.
Basically, you're getting a hotel harborside suite with kitchen for half the price of the bricks-and-mortar kind of hotel. Great bang for the buck.