Yeni Maricela Gonzalez Garcia stands with her children after she was reunited with her children at the East Harlem Cayuga Centers on July 13, 2018 in New York City.

NEW YORK — The children arrive in groups, sometimes many hours after even an adult's bedtime.

Without their parents, often knowing no English, they're brought by federal agents on journeys as long as 2,000 miles from the southwest U.S. border to social services programs operated by nonprofit, religious or private agencies and companies.

Since 2014, thousands of children and their siblings have made the crossing. Coming mainly from Honduras, Guatemala and El Salvador, some were sent by their parents to escape purported violence or other threats. Their illegal trips were aided by smugglers and typically ended with the children in U.S. custody.

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Officially classified as Unaccompanied Alien Children, thousands of the young migrants have been brought to New York City facilities of a company called Cayuga Centers. The nonprofit has received millions of dollars from the federal government during the past several years to place the children in foster care until they can rejoin parents or other relatives.

This year, a new and different wave of undocumented migrant children have joined the federal caravans traveling to Cayuga Centers and other social services providers. They were separated from their parents at the border by immigration agents for weeks as President Donald Trump's administration enforced a "zero tolerance" policy against illegal immigration.

These children also went into foster care at Cayuga Centers, often with their parents having no idea that the youngsters had been transported thousands of miles away. A federal court filing late last week said 364 of 2,551 children between ages 5 and 7 who had been identified for reunification had rejoined their families.

The latest young migrants included a 9-year-old Honduran girl and her 5-year-old sister. They were separated from their mother, Denise Santos, at the southwest border in June after the three crossed into the U.S. Santos asked for asylum and was detained at the Port Isabel Detention Center, near Los Fresnos, Texas.

"We're trying to get them back together," Ricardo de Anda, a Texas attorney helping the family, said in a recent telephone interview.

Amid nationwide protests and court battles over similar family separations, the federal government faces a court-ordered July 26 deadline to complete reunification of all the families. As that process unfolds, Cayuga Centers, like similar social services agencies, has become the focus of an unwelcome spotlight as Americans debate potential solutions for illegal immigration.

"We have nothing to do with the separations. When we take the kids, the kids are already in federal custody," Cayuga Centers' CEO and President Edward Myers Hayes said in a recent telephone interview

David Connelly, who chairs the nonprofit's board of trustees, said he initially feared some might blame Cayuga Centers for the separations or accuse the company of "abetting" the government's policy. He said Hayes satisfied his concerns by asking a question: "If we don't take care of these children, who will?"

If Cayuga Centers is doing good by serving migrant children, it is also doing well for itself. Last year, the nonprofit said it had become "the largest provider of transitional foster homes for Central American children taken into custody while crossing the U.S. southern border."

Federal contracts more than tripled Cayuga Centers' annual budget in recent years as the company provided foster care, physical and mental health screening, schoolteachers and made efforts to return the children to their families.

That income, accounting for what Connelly said was roughly half the nonprofit's budget, has made Cayuga Centers a major provider and financial beneficiary in what has become a nearly $1 billion annual U.S. industry caring for migrant children.

Grants by the U.S. Department of Health and Human Services for shelters, foster care and other services for these children have jumped from $74.5 million in 2007 to $958 million in 2017, according to a recent analysis by The Associated Press.

A surge of undocumented migrants

The still-unfolding crisis began during the Obama administration with a surge of Central American children and families who illegally crossed the southwestern U.S. border.

In all, nearly 250,000 migrant children from Central America were apprehended along the southwest border during the federal fiscal years 2013 through 2017, U.S. Customs and Border Protection data show.

Since 2002, youngsters detained after illegal U.S. border crossings have been placed in the Unaccompanied Alien Children Program, which is managed by the HHS Office of Refugee Resettlement.

Fewer than 8,000 children were served annually during the program's first nine years. However, the numbers started rising in the 2012 fiscal year when 13,625 children were referred to the refugee office. The annual total soared to a high of 59,170 in fiscal 2016 before dipping to 40,810 in fiscal 2017, which ended on Sept. 30.

Some children have been placed in a network of more than 100 shelters in 17 states that are operated by HHS. The youngsters stay there pending release to relatives in the U.S. as they await immigration hearings.

Others have been placed with social services contractors such as Cayuga Centers.

The nonprofit didn't start out to serve undocumented children. Instead, Cayuga Services embraced a revised mission – and financial reward – that arose from the federal fight against illegal immigration.

Based roughly 250 miles northwest of New York City, the nonprofit began its existence in 1852 as an orphanage, according to a history on the company website.

More than a century later, Cayuga Centers expanded its foster care services to serve children placed with the company by family courts in New York. The company added community-based programs and services for people with developmental disabilities during the 1990s.

A history of children's services

Four years ago, the company expanded its foster care programs to take in a new group of clients beset by troubles. The federal government issued a request for proposals to serve unaccompanied immigrant children, and Cayuga Centers submitted a plan, said Connelly, the nonprofit's board chairman.

"Leaving the political debate behind, we asked: What is the humane solution to helping a most vulnerable population of children?" Hayes, the company's CEO, wrote in the Cayuga Centers' 2015-2016 annual report.

In all, 4,215 migrant children who crossed the southwestern border illegally were sent to the company's New York City facilities from mid-2014 through mid-2017, before the family separations began, a review of the nonprofit's annual reports shows. More have followed since last summer.

More than 350 Central American children, including one 9 months old, have been brought to the Cayuga Centers facility in East Harlem since the family separations began in April, New York City Mayor Bill de Blasio said after a June 20 visit to the program. In all, 239 children separated from their parents at the border were at the facility when he visited, de Blasio said.

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Hayes did not challenge the numbers but said federal privacy restrictions barred him from providing a detailed census.

The federal government has awarded Cayuga Centers nearly $92.5 million in contract awards to fund shelter services for unaccompanied migrant children, contracting records show. The awards started in 2014 and are scheduled to continue through the start of 2020, the records show.

The company is paid only for the children who actually receive services and the numbers vary, said Hayes, who added: "We're a far cry from maximizing our contract dollars."

The nonprofit listed a nearly $28.3 million grant for unaccompanied children's services on the 2016-2017 federal tax return filed with the New York State Attorney General's Charities Bureau.

The federal funding powered Cayuga Centers' total annual revenue from $15.6 million in the nonprofit's 2012-2013 fiscal year to nearly $48.7 million in 2016-2017, according to its most recently available federal tax returns.

"We haven't done it for the money. We think we're good at the work, and we think it's good work to do," said Hayes. Despite the federal income, he added that the nonprofit would likely report a budget deficit for its just-completed 2016-2017 fiscal year.

As the nonprofit's revenue rose, Hayes' total annual compensation increased from $186,632 to $244,743, a 31 percent jump.

His total income is comparable with compensation for the highest-paid executives at similarly sized nonprofits, said Daniel Borochoff, president of Charity Watch, a nonprofit sector watchdog. Connelly, the Cayuga Centers board chairman, said in a written statement that Hayes' compensation was "below that of many executives of comparably sized agencies."

Foster care model

Cayuga Centers places the children it serves in the homes of bilingual foster families by night and provides education in the nonprofit's school programs by day.

The Department of Health and Human Services' inspector general's office has not audited Cayuga Centers' contract services and has no immediate plans for a future evaluation, the agency said.

Despite an initial rebuff when he tried to see the Santos family sisters, de Anda, one of the attorneys working to reunify the family, said a social worker at Cayuga Centers' East Harlem facility "appears to be taking care of my client's children well."

However, the younger girl told him her older sister had suffered from a nosebleed and earaches and also cried at night, the attorney said. Cayuga Centers denied his request for a meeting with the foster mother, de Anda said.

"They're not giving us information that's normally received," de Anda said. "If you're the mother and someone else is taking care of your children, you'd like to sit down with that lady and find out what's going on."

Cayuga Centers said that allowing a meeting would have violated a federal Office of Refugee Resettlement regulation.

Separately, a video that was secretly recorded inside the nonprofit's East Harlem facility last month provided ammunition to critics of the family separation policy and also provided a glimpse of Cayuga Centers' services. Obtained by MSNBC, the video showed a young girl identified only as Jessica, tearfully speaking in Spanish as she said she wanted to talk to her mother.

Hayes said federal regulations barred him from discussing the status of individual children. "Kids are different, and they're doing differently," he said.

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The company also issued a statement with its own perspective on Cayuga Centers' services and personnel.

"At any hour of the day, staff are there to ensure that newly arrived youth are fed nutritious food, provided essentials such as clothes and toiletries, educated about their rights, seen by a medical professional to address any health concerns and quickly transferred to the comfort of a foster home in which they are treated with care and respect," the nonprofit said.

However, David Hansell, who heads New York City's Administration for Children's Services, told a City Council hearing late last month that Cayuga Centers staffers "described the depth of trauma, mental health and other issues these children are experiencing."

Hansell pledged his agency's help to provide support services.

Taking a trust-but-verify position, de Anda said he doesn't "necessarily push back" against the company's statements about its quality of care for migrant children. "But I think they need to be more transparent about what they're doing and what's happening to the children," he said.