Police tracked him down after taking the unusual step last Friday of releasing photographs of him but not his name or any other identifying information.
Harrison announced in a tweet Thursday morning that the boy had been found, but a police spokeswoman declined to answer questions about where and how he was located.
Of the two other suspects, only one has been charged.
A 13-year-old boy arrested Dec. 13 and charged as a juvenile with felony murder told detectives he was at the park with the other youths but wasn't the one who stabbed Majors, police said.
Another juvenile suspect was questioned for several hours, also on Dec. 13, but police let him go, Harrison said. He has declined to say why that boy wasn't charged.
Majors was stabbed while walking in the park just before 7 p.m., two days before the start of final exams at Barnard, an all-women's school that is part of the Ivy League's Columbia University.
She staggered up a flight of stairs to street level and collapsed in a crosswalk.
Her death has troubled city and college leaders, both for its proximity to campus and its apparent randomness.
Some city leaders have urged police to use caution in investigating Majors' death to avoid repeating mistakes made with the Central Park Five — a group of five black and Hispanic teens wrongfully convicted of a 1989 rape.
Harrison said in a tweet that the youth taken into custody Thursday had lawyers present "for the entire investigative process."
At a press conference last week, he said the youths previously questioned in the Majors case had guardians present and were told of their right to a lawyer.
The Legal Aid Society, which represents the first arrested youth, said detectives should have waited until he had a lawyer before questioning him.
The organization has also raised concerns about the track record of one of the detectives in the case, saying Wilfredo Acevedo had been the subject of disciplinary findings and was accused in lawsuits of planting and falsifying evidence, lying in court papers and using excessive force.
Police Commissioner Dermot Shea defended Acevedo, saying in a written statement that he had never been found to have made a single false statement or falsely arrested anyone by the NYPD, the city's police watchdog agency, courts or prosecutors.
Shea said the Legal Aid Society was "trying to undermine the case" by singling out Acevedo with "calculated, personal attacks."
In the wake of Majors' death, Barnard and Columbia faculty have reported receiving "abhorrent and viciously racist" robocall messages from a white supremacist organization, and a Connecticut man was arrested after police say he posted online that he was going to kill the suspected stabber.
Majors played in a rock band, sported green hair and had told an editor from a newspaper internship in high school that she planned to take journalism classes in college.
She was memorialized Saturday at a private service at her high school in Charlottesville, Virginia. St. Anne's Head of School David Lourie told mourners that being around Majors left everyone feeling "more optimistic about the future."
- AP
