Hi, I'm flying out of JFK on Thursday bound for Tokyo. Coming from Upstate by bus, I am planning to be at the Port Authority Station around 10am, but my flight is at 12:15! Am I completely screwed? I was thinking I'd hop on the LIRR from Penn Station to Jamaica, and then AirTrain to my terminal. This leaves very little breathing room for what must be a ridiculously busy airport. Is the bus service faster? Any advice would be greatly appreciated!!!

Most airlines require you to check in at least two hours before departure for international flights - some require even longer. Your only option if you want to make the Japan flight is to get an earlier bus (or perhaps a flight direct to JFK?) from upstate. Also, JFK is not a user-friendly airport, so make sure you know which terminal you're flying from.
Good luck!
Pete

I know it's too late for this guy, but it's a topic of general interest.

The Port Authority bus station is at the subway where you can straight away hop on the A train (be sure to catch one to Far Rockaway) to JFK. The Manhattan->JFK trip typically takes an hour from when you get on the train, which practically means it takes a little over an hour from when you get to the subway stop.

There is also a private bus company operating out of Grand Central Station which runs buses to JFK for about $22. (Just ask at the info stand in the main hall of GC where the bus to the airport is and they'll give you directions.) In rush hour, these are slower than the subway but at other times they are slightly faster (~45 minutes from when you get on the bus.) These buses also go to ALL NYC airports.

And to cover other airports, the Amtrak train stops at Newark International Airport if you are coming in by train. (But the Metro North does not.) From the Harlem 125th station (on the Metro North line) you can catch the M60 bus to LaGuardia. And there are various private shuttle companies that run to the airports (look up "airport shuttle" in the phone book.)

Cabs are generally the worst way to go, as they are expensive and not significantly faster.