I believe in Magic/Hopstop.com

How to get around New York without looking like a tourist:
HopStop
It would’ve never occured to me to post about Hopstop.com, but I just found out that Xue and Joe John, two of the most web-savvy people I know, didn’t know about this. I was shocked. Please, do yourself a favor and check it out.
Hopstop is like mapquest, only with subway/train directions, so you’ll never be lost in the city again! It even takes into account the time of day and construction when calculating your route. You can customize it according to your preferences, such as the amount of walking and number of transfers you’re willing to make, or specific trains you want to take, etc… For me, coming to the city for the first time and being absolutely terrified, it’s been priceless.
Note: Hopstop also does Boston, Chicago, San Francisco and DC.