I was afraid about taking the subway and the train to get the airport. New things are always a little bit scary. But it is actually pretty easy! There is a train that stops in all the JFK airport terminals. It is called Airtrain. It costs 5 dolars (plus 1 dolar if you don’t have a Metrocard) and you will see there where to buy the tickets. You pay before taking the train if you are going to JFK and after hopping off if you are coming to the city. The first (if you are going) or last stop (if you are coming to the city) is Sutphin Blv JFK. You will find there also the subway (E line), which is perfect to go to Manhattan or anywhere you need to go.
Indications and signals are perfectly clear so you won’t be lost. Also, there is information inside the Airtrain about the different airlines and their terminals (in case you don’t know which terminal you have to go, this is very useful).
In total, I spent around 1 hour and 40 minutes to get the airport from the East Village. It depends on the subway times of course. Also, take into account that all that I’ve specified here is during “normal hours”. I don’t know what happens after midnight. So if you arrive or leave the city at “late nights”, check the subway stops. Don’t worry about the air train because it works 24 hours.
I highly recommend you to look in Google Maps with the option “mainly by subway” to see how to do it from your place.
There is other alternative that I’ve not experienced. It is faster and a little bit more expensive. Instead the subway, you can pay 7.5 dolars for a ride in a train from Penn Station to Jamaica Center and take the Airtrain there. It will save you around 30 minutes.
Hope it is useful! Have a good flight!
Isabel
