Go see the USS Constitution via the water shuttle, which is part of the subway system! You can take the T to the Aquarium stop; go above ground and take the water taxi. You get a GREAT view of Boston from the water as you go over to Charlestown, for much less than you'd pay for a 'scenic cruise.' Wait in line for the guided tour of the Constitution (it's a security line)- you'll see so much more of the ship than if you do the self-guided tour (which doesn't let you go below decks). There's a Coldstone Creamery right around the corner if you need a "snack" before taking the water shuttle back to the Aquarium!
Duck Tours... not cheap, but one of the best ways to see the city! The guides are knowledgable, fun, and crazy! I grew up outside of Boston and can get anywhere in the city via subway, but driving in the city is nuts. Duck Tours gives you all the highlights AND you get to cruise the Charles River, between Cambridge and Boston. VERY cool!
Sam Adams brewery is accessible via the T. I don't remember what subway stop it is, but it's an easy walk from the T station. We did it in March one year (on St Patty's Day, no less!) and didn't freeze or anything. It's a small brewery, informative tour, and you get a GREAT experience in the tasting room when it's all over!
We liked the Freedom Trail BUT the "extra tour" out to Paul Revere's house is a LONG walk. This is an add-on to the regular tour, which ends at Quincy Market/Fanueil Hall, doesn't have an additional cost, and seemed like a great idea until we actually had to walk it! HOwever, the Freedom Trail tour is definitely worth the money to have a guide instead of just walk the Trail yourself.
BTW, Quincy Market/Fanueil Hall is unfortunately over-hyped and over done. Nothing historical here, just lots of shops (and not much unique... all the usual mall-type stores) and a huge food court. The food part is fun if you are in a group and interested it tasting/sharing, but there's nothing historical about any of this anymore.
There's a very nice holocaust memorial near QM on the way to north station by foot. Very moving, impressive, free. I can't describe where it is, but you should be able to look it up. Worth the time, IMHO.