There is no known record of Rochester-area rioting related to the Revolutionary War or Civil War eras, nor of labor-related civil strife in the 1900s. Nor were any of the Vietnam-era protests sufficiently violent to be termed riots. There were, however, Race Riots in 1964.
1964 Race Riots
In addition to RocWiki's page on the riots, the Democrat & Chronicle did a retrospective series about the July 1964 race riots titled Race in Rochester: Forty Years After the Riots, and Wikipedia also has an article about the riots.
Riots in Other Upstate Cities
Attica, west of Rochester, experienced a bloody prison uprising in 1971.