I've used all three for years, flying every weekend practically. LaGuardia has consistently been the best in terms of service, predictability (i.e. rediculous traffic), being able to get a cab quickly, and ""stuff to do"" at the airport. Only big problem: DELAYS! I'd guess about 25% of flights are delayed. Overall, if you can, I'd go here.
Pros: Close, Clean, Nice Terminals
Cons: Delays, No Int'l Flights, No Subway Access