Two out of three remaining coyotes pups who have been living outside LaGuardia Airport have gone missing — and the activists trying to save them from government hitmen fear the worst.

“I was calling their names and whistling. They usually come out, but they didn’t,” said Rose Ortega, a LaGuardia shuttle bus driver who has been trying to shoo the coyotes away from the U.S. Department of Agriculture agents that have been trying to kill them. “I sat in my car until two in the morning looking for them. I couldn’t even go home. I am devastated.”

The Port Authority called in the USDA to kill the coyotes because they claimed that they were scaring employees who use a lot next to the airport.

The USDA managed to kill nine of the wild dogs last fall, and there were three pups – who the activists named Dumbo, Tony, and Floppy – still alive last week.

Now it appears that only Dumbo, who has extra big ears, has survived.

“I’m despondent at the determination to kill them all even with credible offers to humanely take the animals off their hands,” said Frank Vincenti, founder of the Wild Dog Foundation, who had been trying to get the pups to an animal sanctuary upstate.

Port Authority officials have not yet returned requests for comment about the pups possibly killed over the weekend, but a spokeswoman said last week that the agency brought in the hired guns because it felt the wild animals were a threat.

“Public safety comes first,” said spokeswoman Cheryl Albiez.