Google have today added transit data to New York on Google Maps. Public transit directions are now available on Google Maps for the New York metro region, encompassing subway, commuter rail, bus and ferry services from the Metropolitan Transit Agency (MTA), the Port Authority of New York and New Jersey, New Jersey Transit and the City of New York.
So if you need directions in New York head over to maps.google.com/nyc.
This YouTube video demonstrates how to get transit directions on Google Maps:
Via: Official Google Blog: NYC transit directions have arrived