Are you sure that you are on a Continental flight, as opposed to a "code share" flight operated by another carrier? I do not believe that Continental flies out of JFK.
In any event, the AirTrain ride from Jamaica Station will take about 10-15 minutes to the terminals. (In three minutes, you will not have even arrived at the first stop, which is Federal Circle.) And from Jamaica Station, the AirTrain can depart from either track, as Jamaica is a terminal for AirTrain.
Are you sure that you are on