EWR is newer, that's all. JFK has been around for a LONG time, and has traditionally been a BIG international port. But, EWR is growing very quickly. I often fly out of EWR, and curently, Air France, Continental, Sabena, Lufthansa, United, Northwest/KLM, Alitalia, Mexicana, Air Canada, EVA, Korean, Singapore Airlines, Malaysia, Etheopian Airlines, VASP, TAP, SAS, LOT, El Al, British Airways, Virgin Atlantic, and Aer Lingus all fly out of EWR. (I've probably forgetten a few too.)
So, no, I don't think it's a matter of prestige, but more history. SAS used to be all JFK, and now they're all EWR.