Jerry Chun Shing Lee, 53, also known as Zhen Cheng, was arrested after arriving at John F. Kennedy Airport in New York. A naturalized U.S. citizen, he began working for the CIA as a case officer in 1994 and maintained a top-secret clearance, according to a Justice Department announcement. The department alleges that Mr. Lee and his family left Hong Kong to return to the U.S. While traveling back to the United States, Mr. Lee’s family stayed in hotels in Hawaii and Virginia, where FBI agents conducted court-authorized searches of Lee’s room and luggage, the Justice Department said.