The church exterior was filmed in Noank, the interior was filmed at St. Peter and Paul's Polish National Church (730 State Pier Road) in New London. Tim's house is in Watch Hill, Rhode Island and sits south of the Pawcatuck River (someone told me you can see it from the Watch Hill Inn). Charlie's family's mansion is nested in Stonington Borough.
Thank you! Although I just realized, that when I say "Tim's House" it could be one of two places. I meant the one he lived in, but of course there was also the one he was working on (The Elijas Montrose House). Which one did you mean is in Watch Hill, and where would the other one be (if you know). Thanks again!
I believe both houses were right off Rte. 1 in the Watch Hill/Westerly area in a cove area. I think the one that's visible from the Watch Hill Inn was the Elijas Montrose house, but I'm not sure. Working in the Mystic area every once in awhile, I have found out lots of info. about the movie. Today, I worked with a guy who was an extra in the Planetarium scene. His father was the owner of the red porsche that was driven by Adam Storke. He revealed to me that a replacement car was used in the scene when the lobsters were dumped after Daisy spots Charlie with his sister at the country club. The replacement car (rented from a local dealership) was lined with plastic but fluid leaked through it and destroyed it anyway. If you visit the real Mystic Pizza, there are pictures of the production equipment/cast/crew all over the walls. The movie mockup was on Water Street in Stonington, two buildings before the driveway for Skipper's Dock Restaurant. It still kind of looks like the movie set yet appears vacated right now.