We just got back from there. We bought a 7 day go city pass that got us into a lot places. Our favorites included Freedom Trail guided tour, Sam Adams, Fenway, USS Constitution, Prudential observation deck, and harbor tour. We bought a Charlie pass which got us 'free' rides on the subway and buses. You won't want to drive in Boston. I found walking around a challenge even with Google maps.
A couple of things you may want to skip. Cheers - the outside is being remodeled and that's the part that looks familiar from the show. Paul Revere house - Its old and its small. Do it if you don't have to pay extra but I wouldn't pay the admission price to go in.
In the area, go down to Providence RI, and see the gilded age summer cottages. You can tour the Breakers which is pretty cool.