I tried the AirTrain to Jamaica/E train (subway) combo in both directions this past weekend.
I landed at JFK very early Saturday morning and returned to JFK on Saturday afternoon for an evening flight home. The one-hour timing from midtown Manhattan seems realistic, but I wonder how different it might be on a weekday, especially during peak periods?
In my case, on the return I caught the E train at the 47-50 Sts./Rockefeller Center station (yes, that's right, the E train; it was running partly on the F route over the weekend, owing I guess to construction) just about 4:30 PM. I walked into JFK Terminal 7 (for a UA flight) about an hour later.
Although the NJ Transit train/AirTrain ride from NY Penn Station to EWR is a bit shorter, easier, and more comfortable than the subway/AirTrain trek to JFK, the latter has the advantage of being doable directly from many more points in Manhattan (and other boroughs), since the A and E subway trains cover a lot of ground. This will certainly influence my choice of airports for future flights to NYC.
Kathy