Jason,
Although your list is both sturdy and worthy, the exclusions of any holes from The Country Club, Eastward Ho, Boston GC, and Old Sandwich, Shelter Harbor, Charles River, Salem, Sankaty Head, and even the recently re-worked (by Hanse design) Vineyard GC all seriously delegitimize your thread's title.
Maybe the best 18 of your ventures so far, but I'd go so far as to say that if holes were taken from your picks and included just the above mentioned courses, It would be very, very difficult to find multiple mentions from a single course. It would take hours of time (and thus fewer spent outside playing golf) to do a proper, balanced card all inclusive, however, a far better representation of New England's Greatest 18 would most certainly evolve.
When Boston's MSA is fully examined, it's rich and deep vein of stellar golf courses rivals all but the NY-NJ-CT area. For pure quirk and old-school sporty design on smaller pieces of property, it may well outright own that title.
Cheers