To answer my own question, you cannot search the 1865 NY census as described by FamilySearch; it doesn't work. And I haven't found any shortcuts. Consequently, I have been going through it page by page. This wouldn't be too bad if you have people in a small town. Unfortunately, I am searching for people in Brooklyn. After looking at 504 pages [3 wards], I have found two of the six families I am looking for. Still a long way to go.
BUT .... it is worth it. This is truly a fantastic census. In addition to the usual population data, it includes data on housing, deaths and marriages, and specific data on all current and former military personnel. Also data on handicapped persons [deaf, blind, insane, etc]. Also data on farms, livestock, industry, businesses, churches, newspapers, stores, and bars. Also general economic conditions and other miscellaneous notes [some amusing]. In short, a very highly recommended census.