Citizens and permanent residents go through together and I believe JFK has the APC machines which read the lead traveler's passport and replace the paper form. There may not be too much of a line for immigration, customs is another matter. If you are a green card holder and have been out of the US for more than six months I believe that you should have been getting permission from CIS every six months. I have no experience of this however.

This is not official but it may be helpful: http://www.immihelp.com/greencard/retain-greencard.html