City Hall by Frederick Wiseman.

The House by the Cemetery by Lucio Fulci.

Pieces by Juan Piquer Simon (though, this was mostly shot in Spain. I always get a laugh about them thinking those Spanish exteriors could pass for Boston).

Of course you can't miss an all time classic like The Next Karate Kid.

Radio Boston has been doing a series discussing movies set in Boston: https://www.wbur.org/radioboston/2022/10/27/massachusetts-film-movies-hollywood-noir