Never been fans of rankings. Although I wouldn't say that JFK is the best airport in the country, I wouldn't necessarily say it's one of the worst. It highly depends on the airline, though. The JetBlue and AA terminals are great at JFK: never a long line at security even as a non-elite, and beautiful terminals with plenty of shops and services. Transit access is actually quite convenient for midtown Manhattan - but only if you know how to figure out the Airtrain/LIRR system.
Newark on the other hand, I've always had very long security and check-in lines even as an elite. And access from Manhattan by public transit can be a pain. That dinky monorail is never fun.