As your son is under 18 and if your business is a sole proprietorship or a single member LLC, wages paid your your son are not subject to social security and medicare tax. They are also exempt from FUTA tax as your son is under 21. These wages are subject to withholding taxes, but as they are below the standard deduction for the year, there is no withholding tax. Therefore, you do not have any payroll tax to pay for employing your son.
My advice is to file a form W-2 for him. Just fill in boxes 1, 3 and 5 with his gross wages. Boxes 2, 4 and 6 are left blank.
It is late filing so you may have a small penalty to pay, and you can deduct the wages paid to your son as a business expense.
Please read this IRS document for more information.
You could file a form 1099-MISC for him but he would have to pay self-employment tax.
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