It seems there is very little information about the U.S. Naval Clothing Factory. Even the authors of the reference I used stated the same. The reference used was "American Military Button Makers and Dealers; Their Backmarks & Dates" by William F. McGuinn and Bruce S. Bazelon.
There was more than one such factory. The earliest reference seems to be in an 1886 medical journal where the Naval Clothing Factory at the New York Navy Yard is given credit for improving the health and comfort of sailors (apparently by ensuring they have a standard issue of appropriate clothing). The factory is referred to elsewhere as being in South Brooklyn and was probably part of the Brooklyn Navy Yard.
A New York Times article from 14 August 1899 mentions the “placing of a naval clothing factory on the Pacific Coast.” There is also a reference in a biography of a sailor called Edwin G. Hill that he “served in U.S. Naval Clothing Factory, Navy Yard, Charleston, S.C., from July 26, 1918, to June 2, 1919.”
At some point in time, it appears that the U.S. Navy decided that it no longer needed its own clothing manufacturing operations, uniform production was fully contracted out, and the term “Naval Clothing
Depot” takes over. Clothing depots (as opposed to factories) existed before WWII. The Navy Clothing Depot in Brooklyn was established on 1 July 1933 for example, but the change in responsibility seems to have happened shortly after WWII. The 1947 Navy uniform regulations include a clause that says “Standard samples of uniforms and insignia, as approved by the Bureau of Naval Personnel, shall be kept at the Naval Clothing
Depot.” By contrast, the 1905 regulations say “Standard samples of every article mentioned in these regulations shall be kept at the Naval Clothing
Factory.”
[Credit to Bob Hudson on the US Militaria Forum for this info]