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.
In the aftermath of the riot, organizer Saul Alinsky came to Rochester at the request of local church groups. His account of the post-riot organizing effort is available as part of a 1972 interview.
Riots in Other Upstate Cities
Other upstate cities experiencing race-related rioting in the 1960s included Troy (1966), Albany (1967), Buffalo (1967) and Syracuse (1967).
Attica, west of Rochester, experienced a bloody prison uprising in 1971.