The problem I have with this situation is the way the pilot declared the emergency. He first threatened(sounding like a douchebag) that if his request wasnt met he would declare an emergency. If you actually have an emergency worth declaring you just do it. You don't beat around the bush crying wolf because you didn't get the clearance you wanted.
Sounds to me like the FO was trying to relay what the CAPT wanted to ATC, then the CAPT finally jumps on the radio and tells them to clear everyone.
Wasn't there, don't know what happened. However, that never stopped me from being an armchair quarterback. Guessing some causal factors: closed runways, fuel, high winds, controllers with attitude, NYC, age 65, LCCs, 50% paycuts, long crew days, FAA, etc, etc....
As stated earlier, airline pilots are very experienced and professional, and they don't go blowing thru JFK without a valid reason. Also, sounded like good wx and I'm sure the CAPT knew where the traffic was (TCAS) and knew what he was doing. The question is did he regret it after he landed?