GC Oyster Bar has fried whole Ipswich clams, but I wasn't too keen on them.
Ed's Lobster Bar also has them I believe. But Pearl's and Mary's are probably the places I'd try first.
You probably won't find any that match the clam shacks on Cape Cod, but they will do in a pinch.
Fried whole clam bellies are my all time favorite fried dish, when they are done right.