Well, I think you're right about having to choose one "living" museum or the other. Plymouth (1627) is closer, but IMO Sturbridge (1830s) is much better, much more to see.

so..maybe.....

MOS (1/2 day), with 5 Wits at night

1 day Sturbridge

NEA (1/2 day, and whale watch 1/2 day)

Add?

Swan boat ride

Duck tour

Freedom Trail

Fannueil Hall

Harvard Square (on a Fri. or Sat. night for jugglers, music, magicians and ice cream)

visit to islands in harbor (http://www.bostonislands.org/)

whale watch (1/2 day - combine with NEA visit)

I have 9 year old triplet daughters and we've been to all of these attractions, so I think I can help. I would not do Plimoth and Old Sturbridge in the same three days. Though they are completely different time periods, I think they kids would start to lose interest. We were at Plimoth earlier this month and they definately enjoyed it. They had recently learned about this period in school, so they "got it." Also, the location is better ... beautiful ocean views, marshlands, etc. Buy the combo ticket and check out the Mayflower while you're there. The New England Aquarium is always a hit with my kids. Just try to go during off-peak hours, since it's not as much fun when it's crowded. (Have you looked into buying the Gocard?)

The Museum of Science is also fantastic, the girls are a great age for this. Be sure to check out the Theater of Electricity and definately catch an OMNI movie.

I don't see a lot of "outdoor" activities. Have you thought about walking the Freedom Trail, or the Duck Boats? They might be a little old for the swan boats, but you never know! If you don't do the Mayflower, be sure to tour the Constitution. If you have good weather, consider a Fenway park tour (baseball fans?) or some of those kid-friendly Boston tours. The Mapparium is fun for 9 year olds, or maybe rent rollerskates and roll along the Esplanade?

I would have an itinerary something like this.

Day 1, Duck Tour in the morning followed by a trip to the Museum of Science. 5 Wits in the evening.

Day 2, Trip to Plymouth.

Day 3, Fanueil Hall in the morning then a quick walk over to the Aquarium. See the Aquarium then a Whales & Dolphins in 3D showing at the IMAX there. After that, hop on a 45 minute cruise to the USS Constitution or take a trip up the Prudential Center to the Skywalk Observatory.

A few questions before we can tinker a bit with your itinerary.

Do you have your behind the scene tour tickets already and on which day?

How are you planning to get to Plymouth and/or Sturbridge?

Since you are here for only a short time, I would agree that you should either go to Plymouth or Sturbridge. (Plimouth Plantation is approximately 50 minutes and 43 miles from Boston and Sturdridge is 60 miles from Boston about little over 1 hour away. Plymouth to Sturbridge is about 95 miles apart with a drive time approximately 1 hour and 45 minutes.)

Also, the USS Constitution is a great navy ship, but it is closed to the public on Mondays.