I paid $150 fee online for my visitor visa application. I sent my application package to NY embassy with receipt and came to know that they do not accept online payments.
I don't know the answer to this at all. My wife tells me that the NY Consulate does not accept online payments, as you've said. But does it say so anywhere on their site?
If you want to make sure that the application goes through, you should really call them at (212) 596-1628, and see what they advise you.
I paid $150 fee online for my visitor visa application. I sent my application package to NY embassy with receipt and came to know that they do not accept online payments.