I would say Essex for Mass. personally but that's because I have lots of playing history there. I can see TCC being #1 with the history, the recent work, etc. While Salem is great, I see it at best as #5 behind TCC/Essex/Myopia/Old Sandwich. Salem is neck and neck with Winchester/Charles River/Boston GC, for me, but probably better than those three by a nose.
Maine is tough...it's not Sugarloaf (is it 1995?), and there are many great low-key adventures like NE Harbor/Kebo/Prout's Neck. Penobscot Valley is pretty neat, and so is Portland CC. I haven't seen Sunday River or Augusta CC but I don't see those changing things. Paging Mr. Moore!
New Hampshire is similar to Maine...lots of diverse candidates, and I haven't seen them all. Manchester/Lake Sunapee/a functioning Balsams are the best I have seen. GC of NE is good too, but I have heard Baker Hill is a notch better (have not played it). Never played Bretwood either.
VT...Have played all the relevant courses, and it's Ekwanok by a country mile. Second place? Rutland CC, by another mile. Then a good mix of new like VT National/CC of VT/Green Mountain/Okemo/Jay Peak (have not played that one) and old Burlington/Dorset/Equinox/St. Johnsbury. Those 9 are not in order. It's one 8, one 7, and a bunch of 5s/6s.
RI is a great debate between Newport and Wannamoisett. Both are really, really good. Newport would be my everyday preference, but Wanny is such a great challenge. Gnarlier conditions v. immaculate....might be a draw! Newport needs to fix its bunkers...my last play there in summer 2013 they all had no sand!
CT...I've haven't played enough...about 10 courses only. I have played Yale but not CC of Fairfield so I can't compare those.