These are called archival documents (e.g., a diary, limited-circulation brochure or pamphlet, unpublished manuscript), see the APA Style website for additional examples and explanations.
APA General Format: Author A.A. (Year, Month Day). Title. [Description of Material]. Name of Collection (Call number, box number, file number, etc.). Name of Repository, location.
APA Example: Bradley, M.Z. (1970, June 1). [Letter to XYZ]. Lesbian Legacy Collection Subject Files (Box 4, Folder 1. Coll2009-004). ONE Archives at the USC Libraries, Los Angeles, CA.
The Chicago Manual of Style refers to archival collections as "Manuscript Collections." It says that item identification should be the first part of a citation, and include additional pieces of information to help others locate the item you cite. Most importantly, be consistent in your own work about how you cite archival collections. For more detailed guidance check out sections 14.221-14.231.
Chicago Notes Example: Photograph, "Lisa Ben" [ca. 1965], Box 4, Folder 1, Lesbian Legacy Collection Subject Files, ONE Archives at USC Libraries, USC, Los Angeles, CA.
If you've cited one item from an archival collection, the name of the item or its creator is usually the main element in the bibliography entry. If you've cited more than one item from an archival collection, the name of the collection is usually the main element in the bibliography entry.
Chicago Bibliography Example if using multiple items from the collection: Ben, Lisa, Lesbian Legacy Collection Subject Files. ONE Archives at USC Libraries, University of Southern, CA. Los Angeles, CA.
MLA format from Purdue OWL: Genre-appropriate MLA Citation. Box number, Folder number. Unique identifier and collection name. Archives name, Institutional affiliation, Location. Date accessed.
MLA Example: Bradley, Marian Zimmer. Letter to XYZ. 29 June 1970. Box 4, Folder 1. Coll2009-004 Lesbian Legacy Collection Subject Files. ONE Archives at the USC Libraries, University of Southern CA, Los Angeles, CA. 11 Aug. 2015.
Citing a primary source document from an archive varies depending on the citation style you are using (APA, MLA, Chicago, etc.). Most citation styles require the following information to create a citation: the creator or author, specific item title, page, section, date, box and file number, and the name of the archive.