New York City schools remain closed for the rest of this week, with an estimated 200 of the city’s 1,400 public school buildings flooded or otherwise damaged in superstorm Sandy.

But for schools to reopen as planned on Monday, students will first have to get to them – and the fleets of buses that transport some 600,000 public and private-school students in the city have taken a direct hit.

Monday’s storm surge carried a large boat into a Brooklyn school bus parking lot. Photo: Alyssa Katz

The Bergen Beach, Brooklyn, parking lot for Atlantic Express — a private company that runs about one in four of the city’s school buses — saw a surge of water from Jamaica Bay so high that it carried boats from East Mill Basin over three-foot-high stone barriers and onto the asphalt. Or, in one case, right on top of a bus.

The 30-plus-foot boat Mi’ Lady, registered in Staten Island, perched precariously at a 45-degree angle against the rear of a yellow school bus. And that was not the worst damage in the parking lot. Two other Atlantic Express buses burst into flames after salt water catalyzed in an engine. Other buses on the 105-vehicle lot had motors that wouldn’t start.

Foreman Mickey Hayes, who has been here since the lot opened about three years ago, said that the company’s repair shop nearby had also been flooded, as had lots in Ridgewood, Queens, and elsewhere in the city. Like some other companies with city contracts — another is Jofaz, in Red Hook — Atlantic Express runs hundreds of routes from parking lots located in areas inundated by Monday night’s sea surge. These include Surf Avenue in Coney Island; the low-lying Bronx shore of the Harlem River, and Rockaway Park in Queens.

The company’s headquarters, which include a bus parking lot, sit on the northern edge of Staten Island, directly on the Kill Van Kull and in the Zone A mandatory evacuation area. Phone lines at the Atlantic Express office were not working on Thursday.

The Department of Education has not yet responded to an inquiry about the readiness of the school bus fleet for next week’s commute.

Gingerly, Hayes and his crew in Bergen Beach worked to coax their damaged buses back into action. They propped up hoods to expose soaked engines to air, while casting wary eyes on the ship’s mast looming over them.

“If the wind shifts, this is going to tumble,” Hayes said. “We can’t move the bus.”

He remained optimistic that Atlantic Express would have its fleet ready for Monday’s return to school. “We’re just testing now which ones can go out,” he said over the hum of creaky motors running nonstop.

School buses in a Brooklyn parking lot burned after seawater rushed in. Photo: Alyssa Katz

Atlantic Express is made of tough stuff. In 2008, federal prosecutors told a judge that the company’s founder and CEO, Domenic Gatto, had paid up to $50,000 a year in bribes to the Mafia, because “he feared for the personal safety of himself and his family,” according to Assistant U.S. Attorney Benjamin Gruenstein.

More recently, Gatto was arrested after he allegedly pulled a loaded gun out of his briefcase during negotiations with Department of Education officials over an extension to his company’s contract. (“He did not wave it, he did not point it, and the gun was never removed from its holster,” his lawyer told the Queens judge who heard the case.) He pleaded guilty to disorderly conduct.

The company reports its five year deal with the city is worth about $1.4 billion.