Get a hotel on the freedom trail, that could keep you busy the entire time.
The museum of fine arts is amazing - especially if they have their Egyptian stuff out. Science museum is huge too. Duck boat tours go right by the place but I'm not sure it stops since we always dropped out the boat in the Charles and did the duck boat tour in our own boat.
Catch a harbor cruise, the islands are so beautiful. If you've got time, catch a ferry to Provincetown. Forget the history bit about the pilgrims landing there, Provincetown is a wild and insane beautiful place you will never forget. Although be warned you'll see drag queens in P Town.
Or you could get in your rental car and drive south on the expressway to Rt 3 down to plimouth plantation, keep going and you're on cape cod about an hour out of Boston.
Also south of Boston about an hour and a half is my favorite old city, Newport RI. Newport is amazing to walk around in the summer.
Venus of Crooked Creek 1/26/13
Otto von Hena-C 05/23/08
Morgan Donnermond 08/04/01 to 9/28/12 Long Live the Queen!
I have duct tape and I am not afraid to use it.