Employment Law Questions? Ask an Employment Lawyer.
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It is generally accepted that the labor laws, state and federal, do not cover religious organizations. While all of the labor laws have not been tested by court cases yet, there have been specific findings that the Americans with Disabilities Act does not apply and the department of Labor has said that the Fair Labor Standards Act does not apply (http://www.dol.gov/whd/opinion/FLSANA/2005/2005_09_23_12NA_FLSA.htm).
I have not seen a specific case challenging the NY state labor laws but since the above cases are based on the concept that the government does not have the authority to impose its laws due to the "separation of church and state" section of the US Constitution, the state law can't override a federal protection.