The kids were taken last week, leading to an interstate manhunt that ended in Pennsylvania.
The children will also 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 Nadal, her husband and their seven sons and one daughter since they vanished after an authorized visit to a foster care facility in Forest Hills. That was back on September 19, and it was thought the couple might have taken the children to South Carolina.
Nadal had told a foster caregiver that she couldn't live without her children. Neighbors said she seemed like a very attentive mother.
"A good mother, from what I saw," one neighbor said.
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.
Nadal and Payne were taken into custody at 17th and Berryhill streets in the Allison Hill neighborhood in Harrisburg just after 10:00 p.m. on Monday.
Acting U.S. Marshal Martin Pane said the father has relatives nearby.
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 will be charged in New York City with second-degree kidnapping, first- and second-degree custodial interference and endangering the welfare of a child.