There are many attractions in and near Boston, some of which probably are available on tours from the ship. Here are some possibilities.
>> 1. Museums -- Boston has many, of all different sorts. The major museums include the Museum of Fine Arts, the Isabella Stewart Gardner Museum, the Museum of Science (which also operates the Hayden Planetarium and an I-Max Theater), the Computer Museum, and the New England Aquarium, all within city limits.
>> 2. Colleges and Universities -- The area is loaded with them. The city of Cambridge, on the opposite bank of the Charles River, is the only city to have two Ivy League institutions -- Harvard College and Massachusetts Institute of Technology -- within its borders. There are many museums, galleries, and other exhibits on both campuses. Other major colleges in the area include Boston College, Boston University, Northeastern University, Tufts University, Wellesley College, the Boston campus of the University of Massachusetts, Berkeley School of Music, and the New England Conservatory.
>> 3. Historical Attractions -- The metropolitan area is loaded with them. Since you saw the major attractions in the downtown area on your tour of the Freedom Trail, I won't bother to list htose. In nearby communities, you'll find Plimoth Plantation and the Mayflower II (a replica of the vessel that brought the first settlers to Plymouth), a recreation of the Pilgrim settlement of the 1620's, Historic Salem, site of the famous witch trials of the 1690's (unfortunately, Salem's "witch museum" is more of a Halloween prank than a real museum) but also a historic port, and the "Battle Green" in Lexington and the Old North Bridge in Concord, where the fighting of the American Revolution began, all within a reasonable touring distance of Boston. If the ship offers a tour to Plimoth Plantation, BTW, I recommend it very highly.
>> 4. Boston is also loaded with cultural events. You might be able to get tickets to an "open rehearsal" of the Boston Symphony, where they play the entire evening's program but without dressing for the occasion, if there is one on the day of your visit. Berkeley School of Music, the New England Conservatory, and the School of Music at Boston University often have daytime performances at their concert halls that are very economical. There are also several "broadway" theaters that may offer matinee performances on the day of your visit.
>> 5. If all else fails, you can just wander around the city. The downtown area and the "Back Bay" have quite a bit of architectural inerest. If you get to the Back Bay, be sure to tour the original section of the Boston Public Library, which contains very impressive artwork. Best of all, it's free. The Quincy Market, right downtown, is a nice area to hang out, to shop, and to watch people. Harvard Square in Cambridge is another great place to watch people, and there usually are street performers strutting their stuff. The Boston Common and, directly across the street, the Public Gardens are essentially one large park where you can hang out or even eat a take-out lunch, and the swan boat rides in the public garden also are quite pleasant.
>> 6. You'll find some places to shop in the downtown area, including the Quincy Market, but you might do better at the Prudential Center -- which also has a couple tourist attractions and the Hynes Convention Center, and therefore is accustomed to plenty of visitors. There's an observation deck at the top of the Prudential Center's tower, and the "Duck" tours of the city leave from the back of the Prudential Center. The Prudential Center is in the Back Bay, so you could catch some of the other attractoins there -- including the Isabella Stewart Gardner Museum and the original section of the Boston Public Library -- at the same time.
Have a wonderful cruise!