What are your sons really interested in? There's several years' worth of things to do!
Walk the Freedom Trail; you'll see many of the important historical sites. If you don't so this, at least walk through the Public Gardens and Common. The North End/Paul Revere's House (Italian section of town). The Waterfront, Aquarium. The Museum of Science, Fenway Park. Cambridge/Harvard Square. Museum of Fine Arts.
There are several good walking tours and bike tours you can do in the city. Sometimes it's nice to focus in on one or two and have a guide.
Strawberry Banke and Portsmouth itself are awesome. I would also stop in Portland, Maine on the way up. Similar, but bigger than Portsmouth and quite a foodie town. On the way to Bar Harbor, I would stay somewhere in mid-coast Maine. I love Camden.