Originally Posted by izzik
Instead of walking on the sidewalk under the tracks, I would recommend :
1. Exit the AAirtrain, pass through exit turnstiles
2. Continue on same level through double doors - this will lead you to an
overhead walkway which is above the LIRR tracks.
3. At the end of the overhead walkway, there is an elevator which brings you down to the subway level turnstiles. Use your MTA card to enter the subway and go from there.
No need to be exposed to the immediate area around the station.

I second this excellent advice.