Subway Lines - mattyschell/nyc-spatial-rolodex GitHub Wiki
Open Data Portal
The NYC Department of Information Technology and Telecommunications Geographic Information Systems group maintains a subway lines dataset for use on cartographic products. It's not spatially accurate - editors have used cartographic license to manually separate and generalize lines.
https://data.cityofnewyork.us/Transportation/Subway-Lines/3qz8-muuu
Center for Urban Research at the Graduate Center/CUNY
A parallel effort at the City University of New YorK.
GTFS Data From The Metropolitan Transportation Authority
Good luck. You must accept the counter-intuitive terms to plunge down this rabbit hole.
http://web.mta.info/developers/developer-data-terms.html#data
A description of the challenges using Google Transit Feed Specifications data for subway lines: