Paul,
Take the Airtrain to Jamaica station (you have to buy a ticket - $5 - for this before exiting - very odd) then any westbound LIRR train (not sure how much it costs, probably $7 - head downstairs to get your ticket in advance) to Penn Station. When you get off at penn station, head upstairs one level and head towards 8th avenue (or just follow the amtrak signs). Hope this helps!
Paul, Take the Airtrain to