This user has uploaded 35 videos of old NYC subway and elevated footage. Boston stuff too.
http://www.youtube.com/user/aronsteelo?feature=watch
Check out this 1 hour long video on the IND/BMT Elevated Lines from the 1940s to the 1980s.
http://www.youtube.com/watch?v=DDFc_0qk418
At the 21:59 mark shows the Liberty El at the point of the Rockaway connection prior to that connection being made.
At the 23:42 mark there is a live shot of the Canarsie Line railroad crossing in action.
A lot of awesome footage!!!
Check this one out!!!
http://www.youtube.com/watch?v=bWZcRo8wyO0&list=PLT-i9qfd1kJJ3rARKjrFgA6z8OZPrcXQ9&index=3
Pre-Worlds Fair Flushing line footage.
At the 44:14 mark old SIRT live video complete with railroad crossings!!!
Also old PATH (H&M at the time) and Newark City Subway.
I can't see how this was unnoticed in the past or am I just late to the show.