A few more specifics would be helpful - clam shacks, moderate dining, fine dining or a mix? What states & areas? Actual fish (preferred types) and/or shellfish?
ME, for example, is about half the area of NE. Fresh seafood is typically available throughout, however, within 50 miles of the coast will probably be best.
That said, a few of the best informal places (traveling north long I-95):
Pepe's - New Haven CT - clam pizza
Glenwood Drive In - Hamden, CT - fried clams
Flanders Fish Market - East Lyme, CT - fish
Abbotts - Noank, CT - lobster in rough & lobster roll
Matunick Oyster Bar - East Matunick, RI - local oysters
Spain - Narragansett, RI - Paella
Buttonwood Fish & Chips - Warwick, RI - fried scallops & whole bellies (plus onion rings & fries)
Village Restaurant & Woodman's - Essex, MA - fried clams
Lobster Shack - Cape Elizabeth, ME - crab roll & outstanding scenery
Reds - Wiscasset, ME - lobster roll
Five Island Lobster - Georgetown, ME - fried clams, lobster & outstanding scenery
plus, there are many more fine dining & other full service places for fish dishes along the way (Newport, Providence, Boston, etc).
<message edited by mjambro on Sun, 09/2/12 9:09 AM>