The searches were a result of evidence gathered in the investigation into Faisal Shahzad's alleged bombing attempt, but FBI spokeswoman Gail Marcinkiewicz said that there was "no known immediate threat to the public or any active plot against the United States."
A Mobil petrol station in Brookline, another Boston suburb, was raided, along with several locations in Long Island, New York.
Justice Department spokesman Dean Boyd said the two people arrested were being held on alleged immigration violations, but he would not provide more details.
Shahzad, who is accused of trying to detonate a bomb-laden car in Times Square on May 1, has not yet appeared in court. Federal investigators say he has been co-operating and has told them he received weapons training in Pakistan.
Vinny Lacerra, 50, who lives across the street from the house raided in Watertown, said he was in his living room about 6am when he heard somebody say: "FBI! Put your hands up!"
Mr Lacerra said he looked out his windows and saw 15 to 20 FBI agents with their guns drawn surrounding the house.
He said about 15 minutes later, the agents went inside and came out with one man handcuffed and took him down the street. He also said he saw an agent from Immigration and Customs Enforcement.