AE is in midtown, right? I would really suggest flying into laguardia, but if you can't, go to JFK's webpage for transportation options, which pretty much narrow down to this:
1) the airtran. It's a train that only runs to the airport. Once you get off, you can either get on the subway (I think the E) to get to manhattan, or the long island railroad, which will let you off at Penn station. I think the airtran is aroung 6-8 dollars, and the subway is 2. The LIRR will cost more, but I'm not sure how much
2) Shuttles. Actually, check to make sure you're hotel doesn't have a free shuttle if you are staying in a hotel. Otherwise, there are a bunch of companies ( I think supershuttle is one of them) that run between the airport and the city. They drop off a bunch of people, so if you are the first one off, it's clearly the fastest, and if you are the last... well, that's what you pay for. Around 20 dollars.
3) cab. you'll have to pay an arm and a leg, but it's probably the least hassle and if there's no traffic (and only then), it's probably the fastest.
If you don't have much luggage and are arriving during the day, I would suggest the airtran. But at night, Queens is sketchy.
Just as a note, keep in mind that this is advice from someone who almost always flies in through laguardia.
Good luck.
(In return, can I ask you when you were complete at AE and when you heard back for an interview? Damn, why have they not looked at me for 3 months?! And they refuse to talk to me on the phone and tell me. Shoot.)