Does Ontario have census indexes for the years of 1891 and 1901? If so, is there one or are there several and how can I find one? I am having trouble locating my grandfather (b. 1882), I've looked in the county he was supposed to be born but the family is not there.

Yes there are several indexes available depending upon the year and area of Ontario. Some OGS branches have indexed the census records for their areas. OntarioGenWeb's Census Project also has indexes.

2010 Update:
LAC now offers indexes & images as does Ancestry