The problem involved the computer kiosk check-in system, forcing airline personnel to manually check in passengers at its terminals which led to a ripple effect of delays.
JetBlue said the outage was resolved a short time later around 6:15 in the morning.
But the damage was done.
The outage caused long lines at Kennedy, Logan Airport in Boston and other East Coast airports.
"It would be nice if they people had instructing us what to do," said Lower Manhattan resident Neil Mazer. ('So they're not really telling you what to do/') "No idea. No one knows what line goes where," said Mazer.
The backlog in customers caused JetBlue flights out of JFK to be delayed about an hour.
Airport personnel struggled to get people out as close to on time as possible.
A spokesperson for JetBlue warned delays could last into the early evening, telling Eyewitness News: "Customers may experience some delays throughout the day. We apologize for any inconvenience."
JetBlue personnel tried to counteract the fallout on social media of people tweeting their pictures and frustrations by apologizing directly to customers and saying they would get them on their flights as soon as possible.
The company did not specify how long it would take to work through delays and get operations back to normal.