My favourite is the Portuguese Holy Ghost Society's Lenten Fish Fry. Stonington is home of the last fishing fleet in CT, so the fish is really fresh and they use an ultralight batter that you can taste the fish through. As Stonington is also famous for sea scallops, I recommend the fish & scallop combo
Some other favourites for the rest of the year (mostly during the summer season) are Costello's in Noank, Evelyn's in Tiverton, Cove Fish market in Mystic and Sea Swirl in Mystic. Unfortunately most of these shacks are not 100% dependable as it really depends on who's in the kitchen and who made that batch of batter.
I'll be in New Haven to taste for myself the often hyped New Haven pizza, looks like Stonington is just over an hour from New Haven. Are there fish n chip places in Stonington besides the Lenten fish fry? or should I just go to Mystic (which is closer to New Haven) and try one of the two places you mentioned?