The law guarantees a basic public education as a civil right. If a religious school is not providing a lawful academic program, but is getting federal and state tax dollars, such as transportation, textbooks, technology or special ed funding streams, the local school board (or in the case of NYC, mayoral control) is supposed to oversee the schools and enforce the regulations. One would think some type of audit would be triggered if a complaint was received.

In the rare case of East Ramapo, the public schools were being shortchanged of basic academic services when religious school supporters took over the majority and tried to shift money towards yeshivas. The NY state legislature, governor and Education Department had to step in to appoint monitors in the case of East Ramapo where conflicts persist.

In NYC, instead of a school board, the mayor’s office and Education Dept. would be contacted first. To file a complaint with the NYC Dept. of Education:
http://schools.nyc.gov/Offices/GeneralCounsel/Investigative/OEO/ComplaintForm/

On the NY State level, they have a complaint form for waste, fraud or abuse at: http://www.oms.nysed.gov/oas/fraud/

Or contact the NYS P-12 Office of Accountability here: http://www.p12.nysed.gov/accountability/contactus.html

To file a federal case: https://www2.ed.gov/about/offices/list/ocr/docs/howto.html

But be aware the DeVos administration has scaled back civil rights investigations to the point where they are now being monitored by the US Commission on Civil Rights.

If the USDOE is not doing its job, complaints can go straight to the commission at http://www.usccr.gov/filing/index.php

The Supreme Court just heard a case involving a religious school getting tax dollars which the dissenting justices believe was an affront to the separation of church and state, so religious school supporters are emboldened in the new political landscape to change US tradition in favor of funding religious institutions with federal funds.

Trump has proposed $20 billion in funding for states that expand charter schools and vouchers for private schools, with $10 billion of that coming from direct cuts to public school programs.