The "Train to the Plane" was still running when I joined the NYCTA in 1982. It lasted at least until 1985. i used it a couple of times to get from Jay Street (the station under TA HQ in Brooklyn) to the airport. Usual consist was three R46 cars; the train would open one pair of doors at each stop, and the conductor would stand in the doorway, physically blocking it, and collect the premium fare from each boarding passenger.
As to R44a vs. R46 cars, when I started in 1982, the R44s were all out of service and had been de-trucked, with their trucks placed under 300 R46 cars. Reason was that the R46 was delivered with a version of the General Steel G70 truck that had a radius rod outside the side frame, and the rod tended to break. When that happened, the broken end would flop around and could do serious damage. Several times when I was out walking track, I saw holes punched in signal cases by those rods.
The R44 cars were extremely unreliable for reasons unrelated to their trucks (which were TA standard design), so while new trucks were procured for the R46 fleet, the R44s were taken out of service and rebuilt, and their trucks were used on the R46 cars.
When I left the TA in 1987, the R46 cars had been re-trucked and all the R44s were back in service.
Randy Resor, aka "NellieBly" passed away on November 1, 2013. We honor his memory and his devotion to railroading at railroad.net.