What regulation covers NCOER’s? Specifically where does it say that for a 92Y the commander is the rater and the BC is the senior rater?

AR 623-3.
No reg "specifically" says anyone rates anyone.
It says to stick as close to the MTOE as possible, but the rater should be the direct supervisor and the senior rater is that rater's rater..
In your example, a unit supply NCO does report directly to the CO.
But in most cases, the XO is the one who provides the daily direct supervision.
It is not uncommon for the XO to rate the Supply NCO, and have the CO senior rate.

AR623-3. Rating chain is prescribed by eaters-senior raters

SGT(P) (Join to see) In 28 years every Supply NCO I know of but one was rated by the XO, senior rated by the CDR and reviewed someone in the BN commonly the XO.
The only non-XO rated supply NCO was when the XO was under investigation.
There is no regulation that states specific person rates you as a NCO.

There is generally a LT. who has the supply room as an additional duty. In other cases the 1SG. may oversee supply. In any case they who supervise is they who rates and Senior rates. There is not necessarily a direct correlation between who Senior rates and rates. Company level supply NCOs would almost never be Senior rated by the Bn Cdr.