Agree with others that the A/Howard Beach combo is probably a better ride from WTC, but for someone not familiar with the subways, E might be a better choice as if you get on at WTC, one cannot get on a train heading in the wrong direction or, in the case of the A, a train going in the right direction, but on the wrong line (I made the mistake of getting on a Lefferts Blvd. train once wanting to go to Howard Beach - horrible feeling as you sit on the train and see the Rockaways tracks go by).

If the OP takes the E, all they have to worry about is finding the entrance to the WTC station and finding the E Train platform. Once there, they get on any train leaving that station and ride to Sutphin Boulevard/Archer Avenue/JFK Airport). Since the E starts at WTC, getting a seat should be easier and since the R160A trains run on the E, it's the long bench seating and electronic station announcements that are much easier to hear and understand.