If you have time, the Museum of Science is a fun place with lots of interactive exhibits. For example, they had a room where you could make music and a room where you could spin on something to explore centrifical force. There were optical illusions in another room and so on. They also have a really cool electicity show!
http://www.mos.org/exhibits_shows/live_ ... ions&d=192
We didn't have time to see everything the day we went, because we had show tickets or something that we had to leave for.
Oh, the Mapparium is a must-see! It is a three story stained glass globe with lights that you walk through! The accoustics are fun, too. If someone whispers on one end of the walkway, someone on the other end (or was it in the middle?) can hear him as if he were right next to her.
http://www.marybakereddylibrary.org/exh ... rium.jhtml
Speaking of stained glass - the Trinity Church has beautiful architecture and stained glass windows. There are different styles of stained glass artwork reflecting the changes in style over time. The architect was the first American to attract international attention and the church is one of the 10 most significant buildings in the country according to the American Institute of Architects.
http://www.trinitychurchboston.org/art/index.php
I would advise you to SKIP the Isabella Stewart Gardner Museum. It was dark inside, which made it difficult to see the artwork. I didn't find the MIT museums all that great either.
I didn't go to the TOMB, but it sounded fun.
http://5-wits.com/home.htm
The New England Aquarium is fun. It has three species of equatorial penguins. They don't need to be cold, so they aren't shut behind a glass wall. They can be pretty loud! There is also an IMAX theatre that you can buy separate or combined tickets for. The whale watch cruise is through the aquarium and leaves from a dock right next to it. (There is another whale watch tour run by another group, but I don't know anything about them. I think the tour through the aquarium might help support their research mission, but I'm not sure.)
http://www.neaq.org/penguins/aquarium/index.php
We also saw the Blue Man Group at the Charles Playhouse. It is a small setting and a great show. If you want to see that or some other show, you can get same day tickets for half-price at BosTix. One of the kiosks is by Faneuil Hall. They post a list of whatever they have tickets for for that evening. You have to pay with cash though.
There is always a tour of the Samuel Adams brewery, as well. I don't know your kids' ages, but they might find it interesting. They might get bored while you sample the beers at the end though. The subway goes close to there, so you don't have to worry about driving (orange line to Stony Brook).
http://www.samueladams.com