New England has lots of candidates...
MA...Olde Salem Greens (Stiles), Greenock (Ross)...Whitinsville is private but used to have a public tee time available from time to time, probably less so now with more people playing....Treehouse Brewing operates a 9-holer in Tewksbury now...haven't played the course but the beer is world-class. Highland Links on the outer Cape is appointment viewing.
VT...JP Larkin is a treat, theres another in Bellows Falls that I haven't played that looks neat.
NH...Hooper you mentioned, Carter CC is not bad and a Ross, near 89 in Lebanon.
ME...North Haven!!!, Grindstone Neck, Lucerne, Castine, Wawenock, Wilson Lake, Mingo Springs is 18 but a combination of two old nine holers. I finally played Houlton Community a few years ago and it was fun, with one all-Maine hole. There are a few others that are private that might be playable in shoulder season.
RI...Weekapaug (public off-season), Midville
CT...Fenwick
There are also many old nines with pedigree where a modern nine was added later, sometimes to the detriment of course quality as a whole. Biddeford-Saco, Cape Neddick, and Brunswick GC are three in Maine that fit this bill, all public. I believe CC of Barre and Brattleboro in VT fall into this category too.