I stopped by Custard Beach in the World Financial Center yesterday. They had some Ciao Bella Gelato products on display, so I asked about them. The young woman behind the counter told me that, despite the Custard Beach signs and labels all over the store, all their products were now made by Ciao Bella...no more frozen custard! She said that the store will close next month for renovation, and reopen in the spring as a full-fledged Ciao Bella outlet.
So I guess Shake Shack is the sole remaining frozen custard source in NYC, unless someone knows of another.