Originally Posted by themicah

The Waldorf is very close to Grand Central, and sits on top of the underground rail yards of what is now the Metro North Railroad. The underground Waldorf platform isn't currently in use, but is not exactly a secret either. You can read about it at Newyorkology and see detailed schematics of the track layouts here. There have even been mainstream media news reports that President Bush's security team chose the Waldorf for some of his NYC stays in recent years because they could keep a small train ready at the underground platform as an escape vehicle.

As for JFK, it seems like an unlikely destination for such a train. While there may be a way to route a train from under the Waldorf to JFK via the 63rd St tunnels and a combination of LIRR and AirTrain tracks, there's certainly not an easy way to do it. It would be much simpler to zip the train up to the Bronx or Westchester County where Marine One could pick up W at any number of stations and fly him away to an Undisclosed Location. The main point is just to get out of Midtown Manhattan.