Baer's father, Harold Baer, was a longtime New York Supreme Court justice, born in New York City. The son's own legal career began as an assistant to the General Counsel of Greater New York Mutual Insurance in 1958. He was then Assistant Counsel to the New York State Commission on the Governmental Operations of the City of New York (1959–60) and New York State Commission of Investigation (1960–61). From 1961 to 1967 he was an Assistant United States Attorney in the Southern District of New York. He then served as Executive director, Civilian Complaint Review Board New York City Police Department from 1967-1968 before going back to the US Attorney's office as Chief of the Criminal Division from 1970 to 1972. He was then an adjunct professor at New York Law School from 1974 to 1983.