Originally Posted by maisany
I would say that with the luggage that you've indicated, the AirTrain/subway option would be perfectly doable provided that both of you will have no trouble negotiating a number of stairs with your bags.
As far as your concerns about Monday morning, if your flight is scheduled to leave at 9, you're probably going to want to get there around 7, which would mean you're probably getting on the subway around 6. At that hour, rush-hour hasn't quite kicked in, plus you must remember that for most of your trip, you will be "reverse commuting", thus you shouldn't have too much trouble with crowding once the train leaves Manhattan.
The only difficulty relating to rush-hour that you might run into would be at the subway stop you started from. "Near Times Square" can mean a lot of things and there are a number of subway stations that would fall within that zone. If you start out much later than 6, I would probably stay away from the Port Authority, or the 42nd Street station for both the A and the E trains. This is mostly due to the commuters coming off of buses at the Port Authority, not subway passengers. If you can get started on time, around 6, I don't think you should have too much trouble even at PA.
A cab from Manhattan to JFK would probably run you close to $50, I would think. You can arrange for a car service to pick you up at your hotel for about the same money and skip the hassle of having to hail a cab.
You'll probably be able to leave slightly later if you take a taxi or car service, but not much. This is because car traffic tends to get congested earlier and more easily than public transportation. When there is a traffic jam at the Midtown Tunnel or on the Van Wyck Expressway, it doesn't really matter whether you're sitting on a bus or in a Rolls Royce; you're basically all in the same boat.
This, plus the cost savings, is what is most attractive about taking the subway to the AirTrain.
Thanks for the helpful info.