Shared rides are a great way of avoiding public transport when you have baggage, and are relatively inexpensive (US $ 15-19 one way) when compared to taxis. There will usually be a wait of between 15-30 minutes and the ride time into the city is influenced by how many people are sharing the ride. The transport is provided by a six-seater van with space in the back for luggage. Payment up front (before departure) in cash is required, and tipping is optional, though encouraged. You will be dropped at the exact address specified, be it a hotel or residence.
Ask at the transport desk (located in the luggage retrieval area at Newark & Laguardia, not certain about JFK) or book on-line through www.supershuttle.com/.
Updates
I agree. If you don't have many bags, then by all means, take the Air Train, which, despite having to connect via the subway system, is the cheapest and fastest way into Manhattan. As an international flight attendant who flies out of JFK, I rely on the antiquated NYC Bus Service, but ONLY because I get a good discount. Their service is sporadic, the buses are dirty, the drivers are often rude, and break downs are not unusual--the last one was a month ago when we had an engine fire, and the driver realised that he had no fire extinguisher on the bus!
Is this your business?