Zackary Nazario was found in the vicinity of Rockaway Boulevard and the Van Wyck Expressway, about 16 blocks east of where he disappeared. A Good Samaritan reportedly spotted him.
He is reportedly in good condition and is being brought back to his mother for evaluation.
Authorities say Nazario walked out of his home on Rockaway Boulevard and 118th Street in South Ozone Park around 1:30 a.m., while his 23-year-old brother, who was watching him, ran out to the store.
When he returned, the boy was gone.
Police, several with K-9 dogs, had been searching in alleyways, basements and even opened a locked icebox. A helicopter scoured rooftops from the air.
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