Just to be clear, you appear to be describing a transit (< 24 hours) not a stopover (> 24 hours). In this case AA should be able to check your bags through, and should be able to issue the onward BP in JFK, especially since it is an AA codeshare. If not then you will need to go to the transit desk at BRU to get your onward BP (and remember to tell them that you have luggage checked through).