Uptowners began cleaning up the destruction of Hurricane Sandy on Tuesday, clearing fallen tree limbs, drying out their cars from the pools of water that seeped in during the super storm and finding their way home from shelters.

Neighborhoods in upper Manhattan were spared the worst of the storm, though, which claimed the lives of 39 people nationwide, according to The Associated Press, destroyed homes and left more than 8 million people without power. In New York City, water rushed through the shuttered subway system, spilling over platforms at some stations; the financial district was closed a second day, and many areas of the city were flooded and residents left without power.

About 750,000 New Yorkers are still without electricity, Mayor Michael Bloomberg said, and subways remain inoperable due to flooding.

“Public transportation remains closed until further notice is a good way to think about it,” Bloomberg said. It might be several days before the flooded subway is running again, but limited free bus service was scheduled to begin at 5 p.m. Tuesday, with more buses running Wednesday.

East Harlem faced the brunt of the storm uptown as the Harlem River flooded large parts of the neighborhood. The waters had subsided by Tuesday morning, and there was no visible damage apart from fallen trees and a few garages and store-fronts that had lost part of their facades.

Sandy hit land near Atlantic City, N.J., at around 8 p.m. EDT Monday night, according to the National Hurricane Center. By 9 p.m., the Harlem River had risen over the FDR Drive and swamped the streets all the way to Second Avenue, said residents Teja Frank and Janelle Miller, who saw cars floating on East 100th Street.

Salt water ran underground and blew a transformer outside the Metropolitan Hospital at First Avenue and East 96^th Street. Smoke was still billowing from the building Tuesday afternoon. The hospital has generators, so there was no interruption to care.

“I came out twice during the storm to try and move my car,” said Carlos Revelo, a resident at Metropolitan, who took shelter with wife Leslie Urrutia and their teenage son, Brandon, in the Marriot Courtyard Hotel on East 92^nd Street, leaving the family’s sedan parked a couple blocks down the street. “But the wind pressure was so strong that I couldn’t even close the trunk.” He said water reached the car’s gas tank.

The city ordered mandatory evacuation for parts of East Harlem on Sunday, filling shelters mostly in Harlem near City College.

Three hundred people spent the night at the Nat Holman Gymnasium at City College.  At noon on Tuesday, there were about 50 people dozing on cots and milling around waiting for news on when they could return home. The shelter was still stocked with food, toiletries and medical supplies.

“Looking back, it wasn’t the smartest idea to stay home,” said Rose Bergin who lives in East Harlem. “Many people didn’t take this as seriously as (Hurricane) Irene, but the winds were terrible.” Some neighbors, Bergin said, voluntarily left their homes, but the vast majority stayed home.

Bloomberg said that the shelters would remain open until those displaced by the storm could return to their homes or find temporary housing.

A number of tourists described their night at the shelter as “an adventure” and were busy making calls to relatives outside of New York.

But they and the rest of the city might have a hard time getting around with limited public transportation.

“It affects me and the community a lot,” said Tiro Aguila, 68, who lives in East Harlem. “I don’t have a car to take me from A to B.”

In Inwood, numerous trees were down and the entrance to state highway 9A, as well as to the Hudson River marina, were sealed off by yellow caution tape and guarded by police. But the neighborhood was largely spared the debilitating damage and flooding that wreaked havoc on other parts of the city.

“In this area there’s nothing. Everything’s normal,” said Tobías Perez in Spanish.  Perez said he walked all the way to West 225^th Street, the northern boundary of Manhattan island, to assess the storm damage.

But on Riverside Drive near Fort Tryon Park, far more damage was caused by severed trees and branches, one of which smashed the rear windshield of Rúben Rangel’s sedan. Rangel said he felt lucky that he hadn’t been in the car.

By 11 a.m., many of the businesses on Dyckman Street, the commercial hub of Washington Heights, had reopened. Nick Kabouris, an employee at Pizza Palace, said the store opened at its  usual time after closing five hours early Monday night. Kabouris said he was relieved to find the restaurant undamaged.

“No trees on the roof, no broken windows – thank God,” he said.

So far, he said, Pizza Palace had been doing normal business, but closed bridges and tunnels meant supplies couldn’t be delivered, including a needed shipment of beef patties from Queens.

Jose Naar, who owns Sano Health Foods Center on West 172^nd Street and Broadway, said he did not see any damage in the neighborhood, and his store remained untouched by the storm.

In East Harlem, maintenance workers continued to pump water out of the basement of the Stanley M. Isaacs housing complex on East 93^rd Street, which was flooded up to 8 feet, said residents, who were also without power.

“It’s hard walking down the stairs now, because it’s so dark,” said resident Jessica Byrd, 17. “And it’s really, really cold inside our apartment.”

“See the Con Edison people?” said resident leader of the complex Bergin, pointing at the power company’s truck parked across the street. “They haven’t come here. We are not being assisted by the city because we are public housing.”

In most buildings in the area, though, power was back, and police focused on cleaning up branches and uprooted trees.

Some people were trying to clean up on their own. At Green Thumbs community garden on East 118^th St and Lexington Avenue, Olga Seijo, 77, was picking up broken branches, but had no where to put them.

It was chaotic both before and during the store in some areas. Pioneer Supermarket on East 106th Street accommodated the long lines of customers before the storm.

“Sunday was crazy,” store manager Jason Mercedes said. The store was closed from 6 p.m. on Monday to 1 p.m. on Tuesday, but in that period, someone took advantage of the chaos in the neighborhood and broke into the store.

“The broke in through the ceiling,” Mercedes said. “They got away with … $400  from the register. They tried to get out with a lot of milk and eggs, too.”

Many people had brushed off warnings about the storm, especially after Hurricane Irene caused little damage to the city last year.

“Never in our lifetime has it been like this,” said East Harlem’s Miller, “but now we know it can happen.”

At least one uptown resident, though, hoped the storm would be a lucky strike.  Carlos Ramos headed to the Hudson River Tuesday morning with two fishing poles tucked under his arm. The last time there had been a strong wind, he said, the fishing was excellent.

“Now I’m going to fish,” he said in Spanish. “I’m going to give it a try.”

Reporting by Trevor Bach, Sune Engel Rasmussen, Álvaro Guzmán Bastida and Hollie Slade.