Ditto the Children's Museum and the Duck Tours (You MUST make reservations a week or so in advance in order to be sure to get tix). I would add the Aquarium, which is not too far a walk. It used to be one of the best in the country but has gotten a little tired.
The swan boats in the Common are only a few bucks and great for a little afternoon relaxation. I'd highly recommend them. Let the kids burn off some energy running around the park.
The Freedom Trail is an excellent tour (Bias: I was a Park Ranger for three summers.) but it is 90-minutes and walking, which could make it hard for kids.
Bottom Line: You will not lack for stuff to do with the kids. Let us know how long you will be in town and we will try to map some stuff out.
Mike