We spent a day in Boston recently with a 13 year old. We visited the Bunker Hill monument in Charlestown and the USS Constitution Museum. Both were free of charge. We were walking so we crossed the river (at some locks beside the big bridge). We were able to play the "Charlestown Bells" which is an art installation over a river, that allows the public to play musical notes. We walked from there to Feneuil Hall and Quincey Market to watch the buskers. Then we walked to Boston Common and shopped along the way. We caught the T and went to the Sunset Grill. It was a happening place with over 200 kinds of beer on tap. It was very fun and kid friendly. The T stop is Harvard on the green B line NOT Harvard Square.

I second a visit to the USS Constitution Museum. It is not really a part of the Freedom Trail, but we stumbled upon it on the way from the USS Constitution to the place where we caught the ferry. There is a part of the museum that is VERY interactive for children (it's upstairs, if I'm remembering correctly). It shows what a sailor's life was like-there are hammocks to lie in, ropes to balance on, etc.

We had a very good Italian meal at Artu in the north end. They take reservations and you'll need one if you go at dinner time. They didn't have a children's menu but I bet your kids could split something.