The Q Runner pickup is at the corner of Metropolitan and Lefferts.
Another option is taking the subway to JFK AirTrain. $2 subway + $2.50 Airtrain if you buy a 10 ride ticket.

If you are on the ER and can commute into JFK, then Howard Beach is an option. I've never been there, but I've heard of one or two crashpads in that area.

Once you have access to DeltaNet, go to the Chief Pilot Support Center for the Northeast Region and download the Welcome Package. It's a wealth of information on commuting. The crashpad info is out of date though. Your best source for crashpad info is the message board in the JFK pilot lounge.