Well, you can take the "A" Train to JFK, although that would be a bigger mess (tried that once, took a good 1.5 hours when you factor in the wait time, horrific.)

I don't want to judge people on this forum, but it is kind of funny to hear them make comments about Greater New York area and how "easy" it is to get to JFK, when people like us living in this area for decades know full well what a horrific experience it can be, especially if you are traveling with more than one luggage.