Mohammad Iqbal says agents returned his Pakistani passport and other items they seized in the raid on his Shirley home.
Authorities were looking for possible links to Faisal Shahzad, who they say drove an SUV with a homemade bomb into Times Square on May 1. Iqbal said he never met Shahzad.
FBI spokesman James Margolin confirmed Iqbal met with agents on Thursday. He did not elaborate.
Iqbal said he believed the FBI "felt bad for all the bother to someone who is really loyal to this country."
He had vowed to sue the agency if it didn't apologize.