In terms of frequency, choice of flights/carriers, scope of operations, it
would have to be JFK, closely followed by Newark. However, JFK is not a
very nice place to travel through (unless you fly out of Terminal One,
which is home to Lufthansa, Virgin, Air France, THY, and Olympic, along
several Asian carriers). Improvements are being made to the main
international terminal, and when American Airlines and Delta complete
their Terminal modernization plans, JFK will be a nicer place.
Newark is more compact, newer, and the city's only true hub airport.
Atlanta has a lot of international flights, mostly operated by Delta and
its partners. Connections are probably very good, given that this is the
world's busiest airport (Delta alone operates over 600 flights a day).
For prestige, go with JFK. For convenience, go with Newark or Atlanta.