I believe, even though JFK-EWR are co-terminals, any change to a ticket would require the change fee. Think about it -- if I wanted to change the time of my flight (not the take-off location) and have IT CONFIRMED then I would have to pay the change fee.
I have not booked an AA award ticket in a few years but I belive that any changes require the fee to be paid -- or you may get one change for free.
--Jim