On top of what above mentioned, I would like to advise OP that the underlying reason why you can't clear US customs at YVR is not just because it's leaving too late, it is because the flight is part of HKG - JFK flight. It would be treated as international flight, and thus leaving at YVR international terminal, instead of domestic (where AA and other CA-US flights) terminal.
Also, I've taken this flights handful times in the last 12 months and did not encounter serious delay myself. Usually we arrived before JFK immigration opened and had to stay in the aircraft until about 7am. This by no way means that you should book them as two separate tickets though.