I pulled some GTFS data and pre-computed transit travel times with Open Trip Planner for every intersection in NYC and some urban hubs in the tri-state area. The transit data includes MTA, CT Transit, Septa, and NJ Transit. The polygons are stored with PostGIS, and leaflet makes quick work of rendering them as GeoJSON layers. I have a few mapping projects on the same stack written in clojure/script so it was a natural extension.
Happy to answer any questions.
Note: Most transit agencies willingly provide their own GTFS data, but Amtrak's had to be FOIA'd so I used a third party cleaned up version of it.