At the Newark Airport Rail link station they have ticket counters, however the only company using it right now is Amtrak.
briefly operated check and baggage check there but post 9-11 security ended that, others carriers (UAL, AA
etc) were to also have check in there but security currently prohibits it.
Basically for the few months the check in operation was going on what they did was send the bags down a conveyor belt to a van below the station which drove the bags across the street to the ramp.
Jamaica situation if it ever gets going would operate in a similar manner, van to the ramp.
The only problem is that it can take a long time to drive from Jamaica Station to JFK
on the Van Wyck because of traffic, the Newark Rail link station was only a block away across rt 1 & 9 from Newark Airport.