Original: In 1949, the department was officially divorced from the New York City Police Department, but was eventually fully re-integrated in 1995 as the Transit Bureau of the New York City Police Department by New York City Mayor Rudolph W. Giuliani.
Simplified: It became part of the NYPD in 1995 as the Transit Bureau of the New York City Police Department by decision of New York City Mayor Rudolph W. Giuliani.