I'd also be keen on hearing of other NEC day/weekend trips that are worthwhile since I've exhausted the "major" cities on the route.
If you are not constrained to traveling only the NEC and only by Amtrak then the possibilities are quite a few.
1. Explore Delaware Valley by the NJT RiverLINE from Trenton to Camden. Stop for lunch and exploration at Burlington. Explore the first railroad (Camden and Amboy) in Bordentown. etc.
2. Explore possibilities along the Amtrak Empire Corridor and MNRR Hudson Line. My favorites are Peekskill (MNRR), Cold Spring (MNRR), Rhinecliff (Amtrak) and Hudson (Amtrak).
3. Explore Danbury and the rail museum there (MNRR)
4. Many wonderfulo possibilities on Long Island - Port Jefferson, the Hamptons, Amagansett, Bay Shore ferry to Fire Island etc.
5. Weekend trips:
o Montreal (Amtrak) with possible side trip to Quebec City (VIA) in a long weekend
o Burlington VT (Amtrak)
o Cumberland (Amtrak and Thruway) and the Western Maryland Scenic train
o Altoona (Amtrak) and Horseshoe curve. requires local car rental
o Lancaster (Amtrak) and Strasburg requires local transportation
o Atlantic City day trip or weekend (Amtrak + NJT)
o Saratoga Springs (Amtrak) and S&NC to North Creek
o Charlottesville (Amtrak)
o Utica (Amtrak) and Adirondack Scenic to Thendera and back. (long weekend)
and I am sure a few more that others can think up.