How did the client get your Social Security number? You must have given them a W-9 filled out as an individual, with your Social Security number. As Mike9241 said, if you want payment made to the S corp, give the client a W-9 with the name of the S corp, the S corporation box checked, and the EIN of the S corp. The W-9 is supposed to have either a Social Security number or an EIN, depending on the type of entity, but not both.
For the future, tell the client to stop using your Social Security number and make all future payments to the S corp, with the S corp's EIN. Give them a new W-9 if necessary. When you bill them, put the name and EIN of the S corp on the invoice, and not your personal name or Social Security number. However, if they have already made payments to you this year as an individual, they probably will not be willing to change their records of those payments.
