My husband couldn't get away from the office and my two high school kids were on school trips last spring break, so I took my twin boys (14) to Boston. We had a great time - I highly recommend! It's deserted that time of year, from a tourist perspective, which was great.
My boys loved the Harvard Museum of Natural History - such cool taxidermy and the glass flower specimens are unparalleled. The tour of Fenway was amazing, too - we were not there during baseball season, not sure if tours are offered year round?
We also really enjoyed the Isabella Stewart Gardner Museum, which is within walking distance of Fenway and is the site of the world's largest (dollar terms) art heist in 1990. There is a Netflix documentary that covers the event, and my boys watched it before our trip. The museum is as it was the day after the heist - there are just empty spots on the wall where the stolen art was lifted. It's pretty cool to see.
They also really enjoyed following the Freedom Trail - the whole, long trail - including climbing the steps to the top of the Bunker Hill monument. We did the Boston Tea Party experience/museum, which I thought sounded kind of hokey but was well done and fun.
We loved eating at Giaocomo's in Little Italy - we ate there twice. Also paid two visits to Mike's Pastry. A chain, but we really enjoyed Capital Burger (related to Capital Grille) for a casual dinner. Had lunch at Regina Pizzeria several times (they have a location near Fenway and the original in Little Italy - maybe more as well).
We stayed at the Fairmont Copley Plaza, which was lovely and very convenient to public transportation, Boston Common, etc.
Enjoy! It is so fun to share travel adventures with your kids!