I try to avoid flying out of JFK for several reasons:
Around $50 in tolls to get there.
Heavy traffic in a few areas, especially the Van Wyck Expressway leading to the airport, can really lengthen your trip to the airport.
Expensive long-term parking, $18/day.

However, when I went to Egypt in February, there was no choice. Imagine my shock when I checked out of the long-term parking at JFK and had to pay $29/day! They have a new policy, apparently since last July, that the only way to get the $18 price is to reserve ahead of time online. I don't see how you would find that out, since if you've parked there many times in the past, you have no reason to check. This is just a heads-up for anyone flying out of JFK.

Moved from the Europe Forum

For that kind of money, I would try to fly out of LGA or even EWR to fly to Europe. EWR has its own Amtrak stop so you don't have to park a vehicle at all.

Long Term Parking reminds me of one of The Soprano episodes.

I do try to fly out of Newark, but for the trip to Egypt, there was no choice. I would actually prefer to fly out of Albany, but it is normally a huge amount more. Surprisingly, I am able to fly out of Albany for a trip to Dresden and the Czech Republic this September for about the same as Newark. I couldn't believe it!

My strategy for flying out of JFK (I'm upstate near Poughkeepsie) is to drive to the Poughkeepsie train station, take MetroNorth to Grand Central Terminal, then the subway to where it meets the air train. Sure, it's cumbersome, and time consuming, but it affords me the surety of a non stop flight to Europe, etc.

A bonus is that there are a few parking spots around the Poughkeepsie train station that are unlimited free parking. During a month long trip to Paris, not a penny paid for parking and no parking tickets when I returned...

Have you checked the price of a car service?

Thanks for the heads up Susan. $29 is crazy. We too prefer to fly out of Albany when possible. There are connecting flights on United to Newark but they have a very high delay rate, and over the last few years seem to have a high cancellation rate as well. I've been bitten more than once and now avoid that route. For most destinations we can still connect in a hub like Chicago, Phl, Charlotte, Dulles, Baltimore, or Atlanta. For flights to Europe we've found that driving to Boston is simpler than EWR or JFK.

Years ago when I lived near POK I found that driving to JFK and parking was the best if I wanted to fly to say the west coast or Europe. The train to GC then subway to air-train was more of a hassle than sitting in traffic on the Van Wyck. There were private-off airport lots I tried from time to time, but back then the long term/remote lot by Lefferts Blvd was a lot less than $29. No idea if private lots are still an option.

I think there are still lots close to the airport, but the last time I checked, they had terrible reviews (such as waiting several hours and making numerous calls to get the shuttle to pick them up at the end of the trip).