LaGuardia has the most delays. I avoid it like the plague! You can get from JFK to Penn Station in under an hour by AirTrain and LIRR. You can also take the subway from Jamaica, which may be better, depending on where your hotel is and how much luggage you have. LIRR is more expensive, but more convenient and takes about half the time the subway takes. The AirTrain costs $5 per person each way, plus the subway fare ($2.25 per person each way) or the LIRR fare (depends on whether you're traveling peak or off peak).
If you prefer to take a taxi, JFK has a $45 flat rate fare (plus tolls and tip) from the airport to Manhattan, but you're on the meter for LaGuardia.
There is an AirTrain from Newark, too, which will be much cheaper than a taxi (crossing state lines, you usually have to pay the return fare, as well).
You can also arrange for shared van service. Super Shuttle operates out of all three airports, as far as I know.
There are also buses that run between the airports and major transportation hubs in the City - Grand Central, Port Authority, and Penn Station.