I've been doing the NJ transit from NY Penn straight to the airport, I'm starting to get pretty sick of it as well. Its not the cheapest but they have monthly passes, and 10x trip passes, if you are a line holder its worth the money. I live on the lower east side, I take two subway trains and then the NJ transit train, if I had to do any more transfers I'd kill myself.

If you are coming from Manhattan I would highly suggest getting there in as little transfers as possible, its worth the money.