I don't know about fastest, but the cheapest would be to take the free shuttle bus to Howard Beach subway station, take the "A" train to Penn Station ($2), and then a New Jersey Transit train from Penn to the Newark Airport station ($11.55, be sure to buy the NJT ticket before you get on the train or there's an $5 surcharge.) The free monorail then takes you from the train station to any EWR
terminal, with some nice views of the airfield in the deal.
You can also use the subway to go to Port Authority Bus Terminal instead (one stop further north) and get a bus to the airport. Cost is about the same, and it is likely to take a little more time than the train (but you might get that back by not having to muck about with the monorail - the bus goes directly to the terminal. Then again, if the tunnel is backed up, you might not.)
(Info on the train is at www.njtransit.com, and on the subway at www.mta.info)
The train ride from Penn to EWR
is scheduled for 20 minutes, but the subway ride from JFK
to Penn can be something of a random function - it can take me anywhere from 45 minutes to 1:10 or so to go from midtown Manhattan (two stops north of Penn Station) to Howard Beach, then anywhere from 10 to 30 minutes for the shuttle bus to the terminal. (I can't wait for the AirTrain system to be finished and not have to deal with those stupid buses!) Personally I'd allow an absolute minimum of 2 1/2 hours for the whole ride, since you have to add in waiting time for the shuttle bus, subway, and train. And that's probably a bit tight.
For a faster, but still reasonably priced alternative, Princeton Airporter provides a shuttle bus between the two airports for $24 - go to http://www.goairporter.com/ewk_to_jfk.html for info. They claim 90 minutes between the two airports. You should book this one in advance - walk-ups are first come, first served.
BTW, the subway/train method is not recommended if you have very much luggage - there's no luggage rack on the subway at all, and the overhead rack on NJT can't handle anything larger than a carry-on bag. The train service to Penn is not a dedicated service like Heathrow Express (the best airport train service I've ever used, IMO), and these are just normal commuter trains.
Also BTW, if you decide for some reason to take the bus instead, taking the "A" train one more stop past Penn Station would put you at Port Authority Bus Terminal, where I'd guess the bus for Toronto leaves from.