You've got a great list already and it'll be impossible to hit all or most of these on a short trip, but here are a few other suggestions from someone who's never gotten his mail south of New York:
@garrow's Mystic suggestion is a great under-the-radar choice. The Seaport is terrific and the town is so nice and quaint. And then you can go gamble your 401K away at the casinos less than half an hour away!
For other old-school small-town sights, I'd suggest Sturbridge Village, just over the Connecticut/Mashachusetts border. If you like lobster, you must get to Portland, Maine. (I don't but my wife loves it and still wants to go back 20 or so years since our most recent trip) I've always been fascinated by how far north Maine goes. It apparently gets SUPER rural once you get north of Bangor/Orono (home of the University of Maine). That could be a fun weird trip. Old Orchard Beach just over the Maine border was also terrific when I was a kid, though that was a thousand years ago.
If you want to veer upstate and away from the big cities--and you love baseball--you'll love Cooperstown, especially if you're there in August, b/c the tournaments have wound down and schools are starting to open in the rest of the country so most of the summertime traffic has faded away.
If you want a really cool east coast experience, drive all the way east on Long Island to Montauk Point, dubbed "The End" because, well, it is. It's pretty cool just running out of road. Takes FOREVER, though it's well worth it. Also, some really strange ship happened there in the 1940s and 1950s. Have some fun Googling that!
If you're a baseball fan, my must-see rankings of the stadiums would go Fenway-Camden-Citizens Bank-Citi-Yankee. Fenway & Camden are still jewels and worth seeing once regardless of your rooting interest. Citizens Bank & Citi are nice for new parks and have been around long enough now to develop some character & history. Yankee is a bleak, soulless dump masquerading as the world's most depressing mall. Yankees fans will wax poetic/pathetic about sharing the same area as all the legends of yesteryear, but they were across the street. Go there only if you're a diehard Yankees fan.
As for cities, I love Boston and it's very easy to navigate by foot, public transit or car. You can see most of the sights in two days, unlike NYC...which is fine, regardless of what your lunatic right-wing friends are saying, but it is a lot to absorb and hard to navigate as a newcomer. It is cool walking around midtown at night though. Always has a good vibe, again, contrary to what your lunatic right-wing friends are saying.