More than 500 flights have been cancelled and over 4,000 delayed due to weather and air traffic control staffing constraints in the New York area.
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.
The FAA is slowed traffic in and out of LaGuardia and Newark airports due to the smoky conditions on Wednesday.
Here's what to know about the Air Quality Index and what the numbers mean.