Whoops, I substituted "the camps" for the holocaust by mistake. I got it from mainstream sites(history channel, etc) I'll admit, but the method used was to determine people unaccounted for in the census in addition to nazi records. The ultimate source of the number would come from records that the Eisenhower administration recorded. The method used though, is very similar to how they determine the number of illegal immigrants living in the country.
Rosters or manifests have been found detailing people and why they were targeted next to their name. Many of the people who were declared jews on these manifests would never have considered themselves jewish. Recall Hermann Goering's remark, "I decide who is a jew around here."