Airtrain is not owned/operated by the same agency as NYC Transit, nor were they/are they funded through the same sources.
The NYC Subway is controlled by the MTA and funded through State, City and Federal Taxes. The JFK
Airtrain is owned and operated by the Port Authority of NY and NJ
, it was paid for through a combination of Port Authority Funds and Airport surcharges.
There will be no "free transfer", there could ot be a "free transfer" because there would be no "fair" way of reconciling the two fare structures.
However you can use a pre-paid Metro Card, just as you can with the new World Trade Center PATH station.
The fare to travel to JFK
via the A train at Howard Beach will be $7, $5 for the Airtrain ride from Howard Beach to the Terminals and $2 for the Subway fare. Discounts can count towards your Subway fare, but not the $5 Airtrain fare.
What's not fair is that for the EWR
Airtrain there is a $7.50 surcharge for trips between NYC and the Airport, while the fare for rides from within NJ
are only $5 Dollars. They have such a high surcharge on the NJ
Transit/Amtrak trips from NY so they could have "parity" with the higher LIRR fares, if the surchagre for trips from NYC-EWR
were only $5 Dollars the trip to EWR
from NY Penn would be $2 cheaper (each way) than the trip to JFK
When the PATH is extended to EWR
, they will have a similar surcharge as with the NYC Subway at Howard Beach. It will cost about $7 Dollars to ride the PATH to EWR
airport, that project may start within the next year.
As for getting around the surcharge at JFK
by walking from the Howard Beach Subway to the Long Term Parking Airtrain station, forget about it. The Long Term lots station will be within the confins of the long terms lots fence, the only entrance/exit will be through the "toll plaza". First of all it's a hike, and second I think they do not allow foot access to the long term lots.