An iPhone version of the Android standby, NYCMate offers free, official pinch-to-zoom maps of New York's subways and bus routes.
And once you figure out where to find your transportation of choice, it has schedules to tell you when exactly you should head in that direction.
From the app developers: NYC Mate is the ultimate NYC companion. It has every neighborhood map, bus map and of course.....THE OFFICIAL SUBWAY MAP WITH TRAIN TIMES from Google Transit. !!!!WE HAVE UPDATED THE BUS MAPS, IF YOU HAVE DOWNLOADED THEM PREVIOUSLY PLEASE REINSTALL THE APP TO GET THE NEW MAPS!!!!! WE HAVE SUBMITTED AN UPDATE WITH THE JUNE 27TH SCHEDULE CHANGES AND ARE AWAITING APPLE'S APPROVAL =) IT'S ALWAYS FREE....The goal is to make public information public again. The core application comes with the NYC Subway Map (the new one) and it's 100% hot-touchable. All the other content is downloaded on an is-needed basis.