Authorities searched at least two apartments including one shared by five Afghan men, taking some of them in for questioning, said one man who was questioned.
Members of U.S. Congress briefed by the Federal Bureau of Investigation said there was no imminent danger.
"There was nothing imminent, and they are very good now at tracking potentially dangerous actions and this was preventive," said Charles Schumer, a U.S. Senator from New York who was among those briefed by FBI officials.
A man who identified himself as Amanullah Akbar, a 30-year-old taxi driver, said the FBI raided the apartment he shares with four other Afghan men at 2:30 a.m. (1630 GMT)
He was brought in for questioning and released and said he had no idea why his home was targeted, adding that he believed one of his roommates was arrested.
A neighbor said she saw FBI agents armed with what she called machine guns storm the apartment building, and that one of them emerged carrying a box.
"It was scary. I wasn't going to stop the FBI and ask them what was going on," said Melissa Khan, 28.
NYPD and FBI officials provided few details, calling it part of an ongoing investigation of the joint terrorism task force.