As I was raised in Pennsylvania, I have one point of objection. PA is NOT part of new england. We take pride in not being part of New England.
If you're into the civil war, and your wife can tolerate it, head to Gettysburg. I had a blast there. Every once in a while you might find a piece of ammunition in the field. (which I recommend you turn over to the caretakers) It's informational and educational....so you might hate it if you're not into that. The Philadelphia Zoo is a great spot, and I enjoyed the Boston Aquarium. The Aquarium isn't huge, but last time I was there they had a large gathering of penguins. They also had a good amount of exotic jellyfish that are quite beautiful, especially since a good many of them are luminescent. Avoid Philadelphia's Chinatown. It's just not that interesting. If you're into architecture, the 30th street station in Philly is a nice piece of engineering.
Providence, Rhode Island, is a great spot for seafood. If you time it right you may be there for the Longship festival when they come into port with the old ships. If not there's great little shopping areas, a great restaurant called the Red Parrot, and all the mom & pop eateries that are the real treat. Rhode Island is also home to a few of the old lighthouses, if that's more your wife's speed.
Oh, for Massachussets it might be a nice thing to drop by Lexington. That's where the Minutemen made their stand, and it's located within 5 miles of Hanscom AFB. It's only about 15-20 miles from Boston, and is easily accessed off of I-95. I want to say it's between exit 30 and exit 32. Maybe it was 31b? There's a quaint little town, with great coffee I might add, and a few little restaurants again that I'd love to see again. On the anniversary of the stand the Minuteman society will go out and perform a reenactment. There's a little Indian place down the main boulevard that had some amazing curry.
(I love food, can you tell?)
The wife may enjoy a trip into Faneuil Hall for some light shopping, again with good food, and that place is pretty close to the Boston Aquarium. Feel free to drop by Paul Revere's resting place while you're in Boston since it's very close to a well respected college campus.
I'm out of ideas for now, but I'd like to say BPI had some great points. Best of luck on your trip, and when I think of more I'll submit it.