The LIRR is still running. You could have your cab drop you off at the station or take the airport bus. You will get off at Penn Station. From there, you could take a cab to your hotel.
http://www.mta.nyc.ny.us/lirr/
There's also the NY Airport Service. It's a bus that services Manhattan and the airports-LGA and JFK.
http://www.nyairportservice.com/
You can still get around, but it will be a pain. I'll be heading back to see the wife next weekend. Hopefully, it will be over by then.
[This message has been edited by SFOJFK (edited 12-15-2002).]