16 year old son has now been living with father(non-custodial) for 3 years, in NY state. What procedure is needed to stop paying child support for son to custodial parent?

File a motoin in court for a change in custody ( should have been done 3 years ago) after the change, most likely the court will have the mother start paying support.

But until you go back to court and get the child support / custody agreement changed you will have to pay