At the time of the accident a Navy P-3 Orion was overhead the accident aircraft at 20,000 feet MSL but with the transponder off. When asked by initial FBI agents why the transponder was off they were told it had been out of service for weeks. I find it hard to believe a P-3 pilot would accept an aircraft to go flying around in Boston and New York Center airspace with an inoperative transponder. I am just wondering if turning it off was part of the "classified" exercise with the submarines also in the immediate area. Not that it had anything to do with the accident.