I have found out that there is a cemetery in the Town of Rush that very few people knew about. It is called the Valley View Cemetery and is on the grounds of the School of Industry. There were only 13 boys buried there between 1903 and 1940. All graves are marked with tombstones. The cemetery is not open to the public because of security concerns and it is within the fenced off area.
The School of Industry was originally known as the Western House of Refuge and was formed in 1846 in Rochester to house juvenile criminal offenders. The School bought 1,000 acres in Rush in 1902 and was fully moved to that site by 1907. The early burials from the organization were in a lot in Mt. Hope Cemetery in Rochester.
Update: July 14, 2014
A story in the Rochester Democrat & Chronicle corrects facts for this cemetery. There are 14 total burials. The earliest burial is dated 1909. The cemetery is not in a fenced off area but is on private property. as the land was sold by the State in 1993.