Social Security is 15% - half of which is paid by the employee and the other half is paid by the employer. These amounts would be reflected on his w-2 if he were an employee. He is still responsible for his share even if it was not withheld by his employer.
As an independent contractor receiving a 1099, your son is considered self-employed and pays the full 15% (Self-Employment Tax) - because as a self-employed business owner, he is both the employee and the employer. The restaurant owner is your son's client, not his employer in this situation.
TurboTax can handle his situation either way depending upon his status.
FICA and Self-Employment Contributions Act
Why am I paying self-employment tax?
If there is confusion regarding your son's status, you can get the IRS involved by filing a determination request.
Firms and workers file Form SS-8 to request a determination of the status of a worker under the common law rules for purposes of federal employment taxes and income tax withholding. Generally, under the common law rules a worker is an employee if the firm has the right to control and direct what will be done and how it will be done.
How to enter Self-Employment income
If it is determined he is an employee, enter the income in Federal (or Personal) Taxes -> Wages and Income -> Less Common Income -> Misc Income -> Other Income Not Already Reported on A Form W2 or Form 1099
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