We did the Freedom Trail while we were in Boston, it's a great way to see a lot of the city. It ended with a tour on USS Constitution and a boat back over to Boston.
Have lunch in Faneuil Hall Marketplace, there's everything under the sun in there.
Isabella Stewart Gardner museum is lovely, you can then walk over to the Museum of Fine Art (if that's what floats your boat).
Hop on the train and go to Salem, it's dead easy and it's a beautiful town. You can learn all about the Witch Trials.
The best meal I had there was in a restaurant called Oleana, it's over the river, in Cambridge. If you like Middle Eastern food, it's a must.
I'd love to go back, it's a wonderful city.