I avoid the NJ transit train as I find it more trouble than it's worth. I use the CoachUSA bus to Port Authority. It's about the same cost as the Train and picks you up at the Terminal instead of having to ride the air train to the train platform and possibly waiting 40 minutes like I had to. The busses leave every 15 to 30 minutes depending on day and time of day. Only downfall to this is if you're riding during high traffic time it can take some time but so far I haven't had much of a problem. Then connect to the A/C/E train to the L. I figure you're going to Williamsburg as that's the more common destination on Bedford ave but it does span the majority of Brooklyn. If you're flying CO often in their magazine there is a coupon for $5 off the bus.