Key Takeaway: JFK and Newark airports are both viable options, but the choice ultimately depends on individual needs and preferences. While JFK is closer to Manhattan, Newark offers better transportation options and is generally less crowded.
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LaGuardia Airport: New York's Cheapest, Smallest, & Rather Limited Airport.
Regarding the overall scoring between JFK and LaGuardia, the best option is JFK. Not only has this airport been highly rated for decades, but it's also a better option for international travelers.
Besides the 15-minute AirTrain ride from JFK to Jamaica Station, the transfer to Times Square with the Subway Line E should last around 41 minutes. Thus, the total duration of your ride from JFK to Times Square should be approximately one hour.
Newark Liberty International lies to the west of New York City, and is considerably smaller than JFK, with just three terminals to JFK's six. If your eventual destination is on the west side of Manhattan, a journey from Newark Liberty International will be considerably easier than one from JFK.
AirTrain + Subway from JFK to ManhattanThis is by far the cheapest (and surprisingly easy) option to get from JFK to wherever you are staying. Using a combination of the light rail AirTrain to connect with the subway system is a very easy way to reach Manhattan.