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Another problem with New York and some other airports: the airlines schedule more flights to take off at the same time, than the facilities can possibly accommodate.
"They probably have 20 flights scheduled at the same time, especially in the afternoon," notes John DiScala, a blogger known as Johnny Jet, who flies about 150,000 miles a year.
Nationwide, there are some signs of improvement. Overall, the DOT says 18.7 percent of flights arrived late during the first eight months of this year, compared to 19.5 percent last year and 23.3 percent the year before.
George Hobica, president of airfarewatchdog.com, said that improvement may be due to the fact that many airlines are still operating on reduced schedules because of the recession. That has helped clear up congestion.
There might be another reason. The government bases its on-time performance on the airlines' schedules. So an improvement in delays could be as simple as an airline adding 20 minutes to the flying time between say Houston and Des Moines, even though those cities are just as far apart as they were last year.
"You may be seeing some changes here because of schedule padding," Neidl said.
So what about the worst airport, San Francisco, where the DOT says only 71.5 percent of flights arrived at the gate on time? Well, the airport is sandwiched against the bay, can't add more runways and is often covered in a heavy fog.
"Unfortunately some airports cannot add runways so they are going to have to wait until the next generation of air traffic control," Hobica said.
New air traffic control systems will eventually allow the Federal Aviation Administration to maneuver planes quicker, and with more precision, and therefore space them closer together.
In other places, such as New York, Hobica believes the government is eventually going to need to step in and limit flight slots.
"The airports were built for far fewer flights than actually use them," he said.
Small commuter jets holding 50 passengers take just as much time to take off and land as a jumbo jet with 300 passengers. The airlines might eventually be forced to move away from those cheaper, regional jets.