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.