Dear Ms. Artusa,
Thank you for posting your request on History Hub!
We searched WorldCat and located the Ministries/Institutions collection, 1834-1981 in the custody of the New York State Library that includes some records related to the New York Catholic Protectory. We also located the article At Home in the Bronx: Children at the New York Catholic Protectory 1865-1938 that lists multiple sources in its footnotes. Plus, you may wish to contact the Archives of the Archdiocese of New York, the Catholic Charities Archdiocese of New York, and Lincoln Hall Boy’s Haven for any records that they may have.
We hope this information is helpful. Best of luck with your research!