Flights were diverted and others grounded throughout the Midwest after a temporary outage at a Minnesota air traffic control facility caused issues, the FAA said.
While the FAA continues to limit flights, the number of takeoffs and landings is going up by four per hour to 72, still well below the more than 80 the airport saw before the current caps were put in place.
The FAA has now temporarily banned drone operations in multiple areas of New York, citing "special security" reasons.
Neither of the other major US airlines that historically offered flights to Israel, Delta and American Airlines, have resumed service yet.
Video taken by a passenger shows the flight crew spraying insect repellent as the mosquitoes buzzed around the cabin.
The low air quality and smoke conditions have led to a ground stop at LaGuardia Airport on Thursday morning.