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You're probably better off taking the E if you're worried about the A, and getting the AirTrain at Sutphin Blvd. I personally have never experienced anything bad on the A train, but a lot of people say that it goes through every single bad neighborhood and it should be avoided so meh.
I recently had a 6:00AM flight, which means I needed to be at JFK by 4:30-ish -- which means I had to leave my place in Upper Manhattan around 2:30-ish.
Although I'm usually very comfortable with the subways, I just didn't want to be riding the A train (alone) at that hour. I actually decided to leave the night before, around 11:00PM, and just spent a few hours napping at the departure gate.
If you're very concerned about riding the subway late at night, you should definitely ride in one of the two middle cars, next to the conductor's position. Voicing your concerns to the conductor wouldn't be a bad plan, either; he or she can look out for you. (I say this as a tower operator with MTA--and former conductor for 5-1/2 years).
The E train isn't a bad option, with these two caveats: one, it entails a transfer if you're coming from upper Manhattan. And two, I believe the E train leads the entire system in the number of homeless people on board each train. This may or may not influence your decision.
I don't see what's wrong with the E and AirTrain combo ($7) over the cab.. the E train really isn't bad at all.
The E train is a pretty harmless ride to Sutphin blvd. However its quite nasty (as it most of the subway system at this point). Most of the E trains are old and beat up and the stations are all pretty run down along the way.
Sutphin blvd deserves special credit for its deteriorating, dirty, 1970s style. Its really kind of crazy to think that many people's first experience with NYC after they get off the Air Train is to walk down into the Sutphin Blvd subway station.
Edit: Here's a pic if anyone's interested: sutphin blvd archer ave on Flickr - Photo Sharing! (http://www.flickr.com/photos/darn/307641573/ - broken link)
^^^It's also one of the newest stations in the system, built from the ground up that is. Better looking than most non-rehabbed stations in the system, IMHO.^^^
I don't care how new Sutphin Blvd is, it is still disgusting looking. The MTA is a joke when it comes to keeping stations clean.
Let's put it this way: I'm sure you can think of several thousand better ways to make a living than to work as a cleaner for MTA. It's a never-ending, uphill battle...mostly because, not to put too fine a point on it, many people who use the subway are pigs. There it is, plain and simple. Since I work for the system, I have to deal with this for more hours each day than you do.
They can keep the London Underground pretty clean, because it closes down for several hours each night. New Yorkers love to complain about their subway system, but they wouldn't want to hear about losing the 24-hour service it provides.
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