MERRIMACK, N.H. (CBS) – Elijah Lewis’s mother and her boyfriend have been arrested in connection with the search for the missing 5-year-old boy from New Hampshire who hasn’t been seen in six months.

Danielle Dauphinais and Joseph Stapf were arrested Sunday in New York City on warrants for witness tampering and child endangerment, the N.H. Attorney General’s Office announced Monday. They were picked up by Transit Police in the Bronx. The couple appeared in court in New York Monday afternoon, waived extradition and will be brought back to New Hampshire Tuesday.

New Hampshire social workers reported Elijah missing last Thursday when they didn’t find him at the home he shared with his mother and Stapf in Merrimack. Authorities then issued a bulletin looking for him, Dauphinais and Stapf and they revealed the boy had not been seen by family or friends fox six months.

Prosecutors say Dauphinais and Stapf asked people to lie about where Elijah was living because they knew child protection service workers were looking for him.

5-year-old Elijah Lewis of Merrimack, NH (Image credit NH DOJ)

“We’re trying to find Elijah. We hope we’re going to find him in good condition. But I would be less than honest if I didn’t say that the chances of that are not looking great at this point,” Senior Assistant Attorney General Benjamin Agati said Monday.

Investigators said the boy’s father does not live in New Hampshire, but is aware of what is happening with the search.

Joseph Stapf and Danielle Denise Dauphinais (Image credit NH DOJ)

“At this point, we’re hoping it’s not a recovery mission,” Agati said. “We’re hoping somehow that we are going to go under a rock somewhere and find out that someone has taken him in, maybe there is some sort of mistaken identity that’s going on out there or he’s been misidentified. But right now, we are fearful that may be the direction we are headed.”

Investigators had search dogs out Monday, as they moved from the home where the couple lived, to the pond behind it, to some woods across the street.

“There’s an abandoned house on the other side,” said neighbor Steve Jaynes, pointing to the woods. “Then there’s a camp out in back of that with some cabins and stuff.” He said neighbors never saw the boy. “We never saw this little boy, and several of us are just aghast that there was a five-year-old living there,” he said.

“This is just heartbreaking,” said Greg Doppstadt, who lives next door. From what he knows of the family, he says Elijah’s mother’s boyfriend might be the one to help police solve the mystery. “He’s not the kind of guy that, he’s not an aggressive kind of guy, so at least we’ll be able to get some answers on Elijah, and so that’s a big relief for the people of this community,” he said.

Dauphinais and Stapf are expected to be arraigned Wednesday morning in Hillsborough County Superior Court.

Anyone with information on Elijah’s disappearance is asked to call the Merrimack Police at (603) 424-2424 or New Hampshire State Police at (603) 223-4381 or 603-MCU-TIPS (603-628-8477).

CBSBoston.com Staff