Note: this is a post from last year, updated slightly and reposted here for convenience. Happy travelling!
Figured I’d post up a tip for my fellow bridge & tunnel peeps coming in to Penn Station by rail (NJ Transit, MetroNorth, Amtrak). Check it out — open-source directions! 
The MAKE directions tell you to get on the 7-train (local) and ride it all the way to 111th st. in Queens. Arriving in NYC at Penn Station, however, there is no direct access to the 7. Sounds simple enough, but the NYC subway can be very confusing if you’re not used to it. It is advisable that you periodically check the MTA website for delays or outages, and/or follow the MTA subway twitter feed. Also keep a copy of the maps handy.
When you get to Penn Station:
1. On the east side of Penn Station (7th Ave), you can take the 1, 2 or 3 trains out of Penn and ride them one stop uptown to Times Square/42nd Street. Once there, you can transfer to the Queens-bound 7-train. If you came in on NJ Transit, it’s a good bet you’re on this side of the station.
2. On the west side (8th Ave), you can take the E-train (only the E-train, please do not get on the A or C, which are the same blue color, but which run uptown to the Bronx) and ride it into Queens, where you’ll get off at the Roosevelt Ave/84th Street station. Here you can transfer to the 7. When you’re in the Roosevelt Ave station, you’ll see ads for NYSCI, so you’ll know you’re on the right track. If you came in on MetroNorth, you’re probably on this side. Amtrak is in the middle.
Both of these routes take about 40-50 minutes to get to NYSCI from Penn Station. In my opinion, the E-train is a bit quicker, but there is a surety in being on the 7-train all the way from Manhattan.
NOTE: Please remember to stick to the local 7-train. This has a circle around the number (as opposed to a diamond indicating the express line). If you end up on the express 7-train, get off as soon as possible and wait for the local. The express runs past 111th st without stopping!
MetroNorth Riders NOTE: MetroNorth runs into Grand Central Terminal, which offers direct access to the 7-train. Lucky you!
See you there!