The search for two missing Staten Island boys came to a tragic end today when cops found their remains, police said.

Two brothers, 2 and 4, were separated from their mom on Monday night as she was trying to lead them to safety, away from flooding waters, brought by Hurricane Sandy.

Police commissioner Ray Kelly confirmed today that their remains were found.

“Terrible, absolutely terrible,” Kelly said of the two little kids found today. “It just compounds all the tragic aspects of this horrific event.”

The mom’s car was hit by a wave and got stuck, when she became separated from her kids, police said.

“The car apparently was hit by a wave. Ii stopped, it couldn’t run,” Kelly said.

“She went to get the boys out of the car. Another wave. The water started coming up. She put the two boys on the roof of the car to avoid the water and then another large wave came and apparently washed it away. Of course the mother was totally, completely distraught. She started looking for them herself, asking people to help her look.”

Cops found the boys about 30 yards off the corner of McLaughlin Street and Father Capodanno Boulevard, law enforcement sources said.

The boys were about 20 yards apart from each other, under water, buried by trees and debris, law enforcement sources said.

Since the storm cleared Tuesday morning, cops and other searchers — armed with shovels, sticks and pitchforks — have been scouring those marshlands off Father Capodanno.

Then suddenly at 10:15 a.m.today, searchers dropped everything and rushed to a spot where cops in wet suits discovered 2-year-old Brandon.

His 4-year-old brother Connor was found a short time later.

Also in Staten Island today, an elderly couple was also found dead in their car, Kelly said.

The pair had been reported missing, before their partially submerged car was discovered.

Kelly said he fears the death toll will continue to climb as storm debris is cleared and more bodies are found.

“The numbers are now piling up; the number now is 38,” Kelly said. “I think we have to anticipate it going higher.”

“She spent all night on the steps outside,” said the grandfather, who did not want to be identified. “Nobody wanted to help her.”

The mother was finally able to get help the next morning, when she was taken to a local hospital with hypothermia.

“It was an absolute nightmare,” said Iqbal Mughal, 46, a neighbor who rescued three other people stuck in the flood but did not hear or see Moore as she struggled to find her children.

“You couldn’t hear anyone screaming because the waves were so loud,” another neighbor explained.

“It’s one experience in my life that I’ll never forget,” added a shaken Mughal, who housed nearly 30 neighbors in the second floor of his home, whose first floor was flooded by more than 5 feet of water.

Moore was taken home yesterday morning, where she reunited with her husband, Damien, a city sanitation worker who was in Brooklyn during his wife’s harrowing search for Connor and Brandon.

Neighbors said the beloved parents looked “dazed.”

“They are beautiful little guys,” said neighbor Laurene Ryan, 62, of the boys. “I usually hear them playing in the yard. Connor always had a smiley face. They’re such nice people.

“This is so wrong. This is just unbelievable. There are no words.”

Additional reporting by David K. Li and Leonard Greene