A little out of the box, but Picture a Scientist. It isn’t about Boston per se, it’s about women in science/academia, but faculty at BU and MIT feature prominently. To the extent academia is a huge part of Boston culture and economy, it’s a pretty enlightening documentary. I think it’s currently on Netflix.

Also not about Boston specifically, but the recent documentary Augmented covers Hugh Herr from MIT and bionics/plastic surgery collaborations with Brigham and Womens. It’s available for streaming through PBS.