I was watching Hannibal, and thought I recognized the museum from a visit to Toronto years ago (which is where I know they film most of the show). The episode is called "Naka-choko", but I couldn't' find any of the locations.
Looks like the Royal Ontario Museum of Natural History which is, as you thought, in Toronto. On the page linked, there's a series of stills from the James and Louise Temerty Galleries of the Age of Dinosaurs which includes the image below:
Which looks to be the same room as the second image in your question.