Boston Yacht Haven it is right next to the Marriot Long Wharf. When your there by boat call on channel 9 and you can ask them if they have any slips. $15 per hour and you have to be out by 10:00pm or pay an overnight charge.
The docks in back of the Barking Crab allow you to tie up for free, just pretend like your going to have a couple cocktails inside. In fact, there's no one really there even checking on things.