The shooting happened Saturday night, just before 9 p.m. on White Plains Road.
The NYPD says a 12-year-old and 13-year-old were the intended targets, and were stable when they were taken to the hospital over the weekend.
"I've gotten calls from members of the community who are concerned because this is a frequently used McDonald's in our community, I come here and eat with my children," said Assembly Member John Zaccaro Jr.