You probably won't find one single document of recognition, but rather a whole lot of different court cases and regulations. The Church of Scientology would be a possible case study, because it's quite recent.
Because of the first amndment, there are restrictions on the ability of government to tax religions. For that reason, this .gov publication would be a possible starting place.
http://www.irs.gov/pub/irs-pdf/p1828.pdf
(PDF, 28 pages)