Thomas J. Kinton Jr., the chief executive officer and executive director of the Massachusetts Port Authority, a 1,200-person agency with more than $500 million in annual revenue derived from owning and operating Boston Logan International Airport, two other airports, the public terminals in the Port of Boston, and hundreds of acres of real estate, announced in a letter to employees that he was retiring from the Authority to pursue other interests. With Kinton’s departure, effective June 1, Massport will lose a leader with unrivaled understanding of Massport and how its facilities operate. The Winchester, Mass. resident came to Massport in 1976 filling a temporary job in the engineering department…