Looks like I am answering my own question here, after calling New York State about it.

While you still need to file the Form CT-3-S in order to ensure the fixed dollar minimum tax (based on receipts) is paid, the pass-through entity tax, as of now, can only be filed through the New York State Taxation & Finance website and won't be available until February.  Then, you will file the Pass Through Entity Tax return on the New York State website at www.tax.ny.gov.   If your client doesn't already have a New York State corporation tax online account, they need to set one up, though they most likely already would have had one if they made the election to file under the pass-through entity tax (though they could have elected for 2021 by mail).