Everyone should decide what is best for them.
For some reason, JFK scares me. It's big, under contrucation and it take sforever for buses to get to Terminal 7 for United.
LGA is better, two real main terminals. Traffic can be good or bad. My recommendation if traveling during MOST hours of the day:
Take a cab to the Astoria Boulevard Subway Station. (7-8 dollars)
Take the N train to midtown Manhattan (1.50.)
If time's a factor the cab fare is generally around 12-15 dollars.
As for EWR:
AIRLINK is teh bus that takes you to Penn Station. Runs an average of every 20 minutes.
MY advice: take the tram (as long as it's running) if you are at Terminals B or C to A and get the airlink tehre. The buses and luggage area can fill up fast.
$4 is the fare. best if you don't have too much luggage.
The #62 is also a decent option. But be wraned: the bus drivers insist that you put your luggage under the seat and out of the aisle. SOme can get angry since this bus does fill up with people, students, the elderly. It's also the SAME bus that goes to Woodbridge Center, one of the state's biggest malls.
As Fleetwood Mac sang: You can go your own way..