Josue Zepeda Padilla, 28, had been on the run for more than a year.
He is accused of kidnapping, stabbing and leaving a 15-year-old unconscious in an abandoned building in Brentwood.
The teen victim survived his injuries.
DA Ray Tierney spoke briefly on Wednesday on the gang's violent tactics targeting young people on Long Island and recruiting members as young as 12 years old.
"They're going into the schools, and they're recruiting the kids, they will try to recruit young gang members, and they will start to try to enforce those rules that we spoke about, you know, at the earliest opportunity," Tierney said. "And, unfortunately, what we see with the MS-13, really the drivers of violence in the gang are their youngest members."
Zepeda Padilla is due back in court on April 21 and faces 25 years in prison if convicted on the top count.
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