By this, do you mean that you're on separate tickets? If you're on the same ticket, AA should be able to issue your AS boarding pass at JFK. If not, I'd certainly check in with AS online before your flight leaves JFK. I'd also call AS and have them note your record that you're connecting from AA. Not sure how much that will help, but AS has always been happy to make that note for me when connecting from a separate ticket, and the AS web site now even shows that there is a linked reservation. Fortunately, I've never had anything go wrong in this particular situation, so I haven't tested whether that note is worth the electrons it's written with.