The search continued in the days that followed, with numerous emergency personnel joining the march through Staten Island marshland. The bodies were found about 100 feet from each other at the end of a narrow dead end street.
Television video later showed the water-logged SUV, two children's car seats visible through a window.
Damian Moore, the boys' father, reached on his cell phone, said he had no comment about the tragedy.
The boys were among 19 storm victims found on Staten Island, out of nearly 40 who died in New York City's five boroughs. Those identified Thursday included a couple who apparently drove away from their home as the storm struck.
The 89-year-old man and 66-year-old woman were found lying next to a car in a vacant lot. Police believe they drowned after climbing out to escape rising water.
Authorities stressed that the death toll was preliminary, and that the total could change if the medical examiner determines any deaths were not storm-related.
Associated Press writers Jennifer Peltz and Tom Hays contributed to this story.