You might try the aquarium. And head out to see Lexington and Concord (if your kids don;t know about the start of the revolution and what happened there is long past time that they learned - and saw a little of it.)

IMHO, learning should always be a part of any vacation with kids - this is how you teach them that learning is FUN, and a continuing part of everyday life. Otherwise you can end up with kids who don;t love learning, don;t love school and want to spend their lives playing video games. It's really important to start this early - my parents would take us to the city at least once a month to visit various museums and exhibits - even when we were way younger than yours.

How about the laser light show at the Museum of Science. Check to see what movie they are showing. Our 4-H kids loved the laser show.

I agree that learning should be part of vacation. The North End is a fascinating neighborhood. Find the litte shop that sells lemon ice. Try a real Italian sandwich.

Chinatown is also fascinating. Take the kids to a dim sum lunch at one of the big restaurants with rolling carts. The waitresses usually don't speak much English. You point to what you want. It's all small plates, usually 4 small servings. Try a Chinese bakery. Have bubble tea. Although coming from NYC you are probably familiar with a Chinatown.

Ducks tours are usually fun. I'm afraid I went on too many school field trips to parts of the Freedom Trail. The Prudential skywalk might be fun.
http://www.boston-discovery-guide.com/prudential-skywalk.html#axzz22bMcjSsq

How about Harvard and the Harvard Museums (anthropology, natural science, and the amazing glass flowers)? Eat at Mr Bartley's in Harvard Square.

How about a walk along the Charles River esplanade, down Charles Street and across the Public Garden to the Back Bay? Include a ride in the Swan Boats.

Charlestown Naval Yard and Old Ironsides by water taxi from Long Wharf.

Trips to the Boston Harbor Islands can be fun. Fort Warren is interesting for tours, guided or self guided. Lots of climbing and views. There are also whale watch tours out of the area near the Aquarium.

Thanks all- this all sounds good. My son loves history so we will definitely be checking out those revolutionary war sites. Have to look into how far Lexington and concord are. Thanks again

If you're not renting a car - and it's a very bad idea for tourists to drive in Boston - I think the Gray Line has tours to Lexington and Concord. Lexington is about 30 min+- from Boston, depending on traffic. Concord is a little farther west but the tours would take time but are interesting. Having said that, there are many Rev War things to see in Boston along the Freedom Trail. Going out to the burbs might take more time than you'd want to spend. Fort Warren on Georges Is in the harbor could be a great idea if you all want to get out on the water away from the city for a few hours.

1ststreetmom, will you have a car on this part of your trip? It's not needed - but if you don't have one, I'd leave Concord and Lexington out on this trip. In fact, for a summer vacation, going out to at least one of the islands in Boston Harbor would be preferable to those landlocked towns! (If you do go to the suburbs, take swimsuits for a dip in Walden Pond in Concord.)

There is a ton of history on the harbor islands; I remember our junior high school field trips there were a fun combination of easy hikes and history.

Another suggestion is the Mapparium in Boston. Make a reservation in advance so you don't have to wait around to enter; the whole thing will be less than half an hour but it's so cool to stand inside the large glass globe! The cafe just off the lobby has yummy chocolate cake.

Honestly, with only TWO DAYS, you will barely have enough time to do the Duck Tour and walk the Freedom Trail. I agree with heading over to Harvard Sq on Cambridge side. These 3 activities will take up your entire 2 days.

I would definitely skip Concord & Lexington on this short trip, and while Harbor Islands are nice in the summer, they will easily take up half a day or more...

The Science Museum is a terrific spot, though it is always busy. Some of the duck tours begin there, so it might be very convenient place to visit. My kids always loved it.