When we go to WDW, Delta usually has the best choice from New York (LGA). We've had great experiences with them. But we also really like American Airlines when going somewhere other than WDW, and their schedules are pretty good, and we like the flights a lot. They also seem to have the most non-stop flights. We had to go to St. Louis a few months ago- you'd think that wouldn't be too hard, but every other airline had us doing at least one connection. American was direct (from LGA or JFK) for less money. Also, their flight from JFK to London is usually one of the better priced one, and the service is excellent. Their website is really easy to use, and tends to have cheaper fares than by phone.
If we're going somewhere that JetBlue can take us, we'll usually go with them, as the flights are great, and their web fares have been the best each time we've used them.
I wish Southwest flew out of an NYC airport (Hartford, CT is too far), as they really seem to be good.