One of the hidden gems of Boston are the Boston Harbor Islands. If you have an extra day (or half day) on your trip, consider going. There are 34 islands in all, 24 with archeological activity on them. Not shockingly, Native Americans used these islands before we settlers did, for hunting, farming and other activities. You can visit 12 of the islands.
Even their recent history is interesting. The country's oldest lighthouse was first built here in 1716, though the British burned it down in 1776 and rebuilt in 1783. That makes our own Sandy Hook lighthouse (built in 1764) the oldest working lighthouse in the United States. You can tour the lighthouse on Little Brewster Island on a different boat tour, along with two other lighthouses.
The popular Spectacle Island is only a 15 minute boat ride from Boston's Long Harbor. On the way, they gave us interesting information about the islands, which are a National Park area (though the boats are an outside vendor). If you flew into Boston, you'll likely have come into Logan Airport, also known as General Edward Lawrence Logan International Airport, named after a Spanish-American War officer who had obviously never been on a plane. More relevant, though, is that Logan takes landfill from three of the Boston Harbor islands: Governor's, Noddle's, and Apple Islands. Planes land on average every 30 seconds, and we saw quite a few overhead on our boat ride.