Knowing what I know about public transportation to the airports, I always budget way, way more time than I need. Weekends and early mornings can take forever if there is track work going on.

I also always use the Jamaica station route rather than Howard Beach even though I live in the Village/Chelsea area. If the subway has a problem I can get on the LIRR (happened to me one time when the trains were stopped at Kew Gardens from going on) and its usually easy to find a gypsy cab at Jamaica station if there is an issue with the Airtrain (happened to me a couple of months ago).

Also, as nerd pointed out get off at T1 and take the inter terminal train to T8 (about a 15 second ride.) HOWEVER, ALWAYS CHECK THE MONITORS AS THE PA IN ITS GREAT WISDOM WILL TAKE THAT TRAIN DOWN DURING PEAK TIMES OR HAVE IT RUN THE OTHER WAY.