pseydtonne, I think you might like this. I'm actually going to Berlin in two weeks, and NYC in four - I'm not complaining!
I'm deeeeeeeeeeeeeeply envious of your trip to Berlin. I hear the ride to the Zoo is one of the most beautiful transit trips aside from the 2/6 circuit in Paris and the E train from the Hague to Rotterdam (where I saw sheep and shepherds out the train window). If you haven't been to NYC before and you're flying into JFK, you'll get the privilege of the SkyTrain. If you're staying in Midtown, pay the $7 for the LIRR from Jamaica to Penn Station -- 22 minutes and you're in the middle of it. Oh, and don't be afraid to ride the 1 train up to Marble Hill. This is one of the most mind-blowing views of sculpted rock, the Pallisades, cast-iron bridges, and the only part of New York County that is no longer on the island of Manhattan. On your way back, visit the Cloisters.
I'll look into it! I'm planning to get on at least every one of the colored subways once. Also gonna get a MetroCard - I can use it to get on the train from Jamaica to Penn too, right? Getting to Berlin is gonna be sweet too, since most of the trip is in a nice ICE train. Hotel is right on top of a U6 station. Don't have too much free time though, there's a reason I gotta be there.
You can use your Metrocard on the SkyTrain (from JFK to either Jamaica's megastation or to Howard Beach on the A train) and on buses and subways, but not on the LIRR (commuter train). The easiest thing to do is buy a Metrocard when you get to the SkyTrain station at your terminal. Put both a week's pass and $10 on it. The first $5 will be taken when you exit the SkyTrain turnstiles at Jamaica (it's free when you're going from terminal to terminal, but they charge you at the non-terminal stops). The weekly pass will kick in when you first ride a bus or subway. While you're exiting Jamaica's SkyTrain station, grab as many maps as you can. The subway map is obvious. However the borough bus maps are also really good walking maps. Get two Manhattan bus maps -- one to mark up and another for your wall.