The siblings - who range in age from 11 months to 11 years old - appeared to be in good condition, police said. Their parents, 28-year-old Shanel Nadal and 34-year-old Nephra Payne, were taken into custody in Harrisburg.
The children will be returned to New York City and receive any needed medical care and counseling for any trauma they experienced, the city's Administration for Children's Services said.
"An investigation by ACS is already under way into how the children could have been abducted from the foster care agency during a supervised visit," Michael Fagan, an agency spokesman, said in a statement.
Authorities had been hunting for the children and their mother since Sept. 19, when they disappeared from the 3-acre campus of Forestdale, a nonprofit, privately run foster care center in Queens.
Nadal went to the center for a scheduled group visit with the children, who had been placed with three different foster caregivers. Despite the presence of both Forestdale staff and at least some of the foster parents, police said, Nadal slipped away unnoticed with the children during a trip to a vending machine.
Forestdale officials wouldn't discuss the situation with The Associated Press, but the agency's executive director, Anstiss Agnew, told The New York Times in an interview last week that neither the family visits nor the facility had been set up with security in mind.
"I guess we could put up bars and put up a moat," she said. "We're trying to heal family here."
Acting U.S. Marshal Martin Pane told the AP that the investigation led them to spot the family's van in Harrisburg on Monday evening, when it was parked on a Harrisburg street. The father has relatives nearby, he said.
As officers kept watch, Nephra Payne was seen coming and going at times with some of the children, authorities said.
"Our initial concern was, where were the other children? But ultimately the van was searched, and all the children were in there," Pane said.
The children showed no signs of physical abuse, he said. They were placed with a child services agency until they can be returned to New York.
The father collapsed at the scene and was taken to Harrisburg Hospital, where he remains in medical custody, Det. Sgt. Dave Hodges of the Dauphin County district attorney's office said Tuesday. Payne was expected to be released Monday and be arraigned and taken to the county prison.
Nadal was arraigned earlier and is being held on $200,000 bail. New York City detectives, along with Hodges and others, interviewed her in Harrisburg on Monday. Hodges declined to disclose anything she said.
The parents are charged in New York with custodial interference. Hodges did not think that any additional charges had been filed in Pennsylvania.
The couple had lost custody of their seven sons - all named Nephra, with different middle names - in 2009. They subsequently lost custody of a girl born last year. Authorities in New York have declined to say why they seized the children, but the U.S. Marshals Service said it was because of an abuse allegation.
Parental abductions of children in the foster care system do happen from time to time, often involving mothers or fathers who fail to return a child from an unsupervised visit.
But the disappearance of the Payne children garnered extra attention in New York because of the number of children involved and the nature of the family's exit from what was supposed to have been a supervised setting.
Barbara Emanuel, a foster mother who had been caring for the girl, Nefertiti, and was apparently the first to notice that the family had fled, told reporters that she couldn't understand how it happened.
"It's like they just vanished," she told the Daily News of New York shortly after the disappearance. "How does a woman escape with eight kids? I was there and I don't know how she did it."
The Administration for Children's Services, which has a contract with Forestdale to run part of its giant foster care system, said an agency staff member should always be present during supervised visits.
City police had said the parents might go to South Carolina, where they once lived.
New York City police contacted the Marshals Service on Monday to say the family might have moved on to Harrisburg. Both New York City police and the U.S. Marshals took part in the arrest.
"It appeared as though everyone intended to spend the night in the vehicle," the Marshals Service said in a statement issued Tuesday.
Associated Press writer David B. Caruso in New York contributed to this report.