Howard Beach-JFK Airport was recently completely rebuilt in order to incorporate the connection to Air Train that exists in the station's mezzanine. Before AirTrain opened in 2003, the station was very poorly designed for travelers transferring to the Port Authority Shuttle Buses to the terminals. Formerly travelers trying to reach the airport terminals from Rockaway-bound trains had to get off and use the overpass at the main station house at the southern end of the platforms (on an overpass above them) and then walk the length of the uptown (Manhattan-bound platform) to another station house (at its northern end) and use an exit along the uptown platform at street level in order to transfer to the shuttle buses.
Today the transfer to AirTrain is much more easy from the completely rebuilt and ultra-modern looking station. The station has a large modern glass mezzanine above the tracks with stairs, an escalator (down to the Brooklyn-bound, up to the Rockaways-bound platform) and two elevators down to each platform. The AirTrain entrance is to one side with its fare gates that require the five dollar MetroCard AirTrain fare, there are some AirTrain fare gates that lead directly from the subway portion of the mezzanine to AirTrain deducting $7.50 (Airtrain fee plus subway fare) from people transferring from AirTrain to the subway, ($5 going the other way from the subway onto Airtrain). There is a central booth with windows to all three sides of the station. Token clerks. Unlimited ride MetroCard holders can use the other fare gates with a pay-per-ride MetroCard to completely leave the AirTrain and subway systems and reach 3 regular subway turnstiles to enter the subway system. For community access to the west of the station, there are two high entrance turnstiles to Coleman Square from the Rockaway-bound platform, as well as 2 elevators and stairs (that are accessed through an unmarked door and feel like an emergency exit) down from the mezzanine area outside of fare control. The platform signs also have a bit of an unusual design on account of the AirTrain Station, in addition for some reason the platforms are offset a bit with the Manhattan-bound platform farther south than the Rockaway-bound one. Just north of the elevated AirTrain Station, along the Manhattan-bound platform is a wide Emergency Exit Gate.
This gate is relevant because it leads directly to a small bus loop in the station parking lot normally used by Shuttle buses to the surrounding Long Term Parking lot with passengers accessing the buses from the exit at the AirTrain platform opposite the subway entrance (that is free since your staying on Airport property). This gate is opened during construction when A trains terminate at Howard Beach to and from Manhattan and Shuttle Buses are required across Jamaica Bay to connect with S Shuttle Trains running between Rockaway Park and Far Rockaway via the normally unused Hammel's Wye. Normally on two routes: one via the Cross Bay Bridge to Rockaway Park via Broad Channel and Beach 90 and 98 Streets. Another runs via Nassau County non-stop to Far Rockaway. Subway Fare collection is accomplished using a couple of bus fare boxes that are set up and manned by attendants (plus GO transfers used by passengers who have paid their fares for the Rockaways Shuttle). A MetroCard Van is parked outside the entrance for MetroCard sales (there is no access without paying the AirTrain fee to MVMs inside the station).
Superstorm Sandy: The rail line across Jamaica Bay was surverly damaged during Superstorm Sandy and A train service was first restored to Howard Beach on Sunday, November 11, 2012 with connecting bus service only to Far Rockaway via Nassau County (leaving through the parking lot). Starting on November 20 this bus connected to free H Shuttle Train service (to negate the need of dealing with paper transfers) running from Far Rockaway to Beach 90 Street. No Shuttle Bus service has been provided to Rockaway Park. This long term service change originally saw the usual bus fare boxes used to pay fares but eventually a small temporary shack of basically scaffolding was built beyond the emergency exit gates. This covers three turnstiles (one still has a trubo-turnstile on it left over from that experiment). An open slam gate is used by exiting passengers.
Subway service south to the Rockways was restored on May 30, 2013, around Noon. At 10:41am the R1-9s led by R1 #100 with a "Rockaway Here We Come!" sign to make a dignitary run to the Rockaways with press and me aboard. As of July the scaffolding is still up but all the turnstiles are gone at the makeshift entrance. One consiquence after Sandy is the normal relay track used by the Rockaway Park Shuttle just north of the Broad Channel Station is still out of service (as of July 24) this requires all Rockaway Park Shuttle trains since service was restored after the storm to make extremely long relay runs across the North Cannel Swing Bridge and onto the mainland, and relay in the middle tracks at Howard Beach-JFK. This has caused gaps in Rockaway Park Shuttle Service (instead of the normal clockwork A train arrives, Shuttle train follows it) service.