One is http://www.southwest.com and likely http://www.usairways.com as well. Be sure to factor in the additional costs of getting to/from Manhattan if you fly into ISP. It's often not worth it unless the savings is at least $100.

I would also recommend checking http://www.ata.com. National Airlines serves LAS-JFK non-stop, but personally I wouldn't give my money to an airline that is in bankruptcy proceedings, especially if you wouldn't have the means to buy another ticket if they cease operations.