In 1844, Parker moved to Albany, New York to accept appointment as judge of the New York State Circuit Courts' Third Circuit, a post he held until the circuit courts were abolished in 1847. Parker presided at the 1845 trial of Smith A. Boughton (Big Thunder), a leader of the tenants during the Anti-Rent War. Parker declared a mistrial, and the retrial was heard by John W. Edmonds. the second trial resulted in a conviction, and Boughton receiving a life sentence, which was later commuted by Governor John Young, who had been elected with the support of the tenants.
