I just flew out recently and it took... maybe a half hour to check my bag and get through TSA security with an opt out request (for the scanners, so they pat you down instead).
Maybe I'm lucky, but I've flown through JFK and LaGuardia a fair amount and never really had any staggering wait times.
I do wish they could have just made the Air Tram part of the subway system cause taking a taxi during rush hour was certainly a mistake but Q ->... hmm I guess the A or J or whatever train would get me to the Air Tram -> Air Tram is a bit of a pain.
Although, I will say, if you stand at the front of the air tram at night so you can look out the front window as you zoom down the track, that's pretty neat and beautiful.