It's 40,000JPY NRT-JFK and you can do it at the check in counter, don't have to wait until the gate.

https://www.jal.co.jp/en/info/inter/apopyug.html

I've done it, but not on that specific route. As for if they're always available, I'd say it depends. JAL doesn't hold seats back for paid upgrades so if they (or their codeshare partners) sell every seat, they're gone.