I am an international student. I have a W2 from 2 employers and a 1099 Misc. from another employer. I qualify as a non-resident alien. The following is my question.

On the 1099, it doesn't pay me as wages, but as self-employment compensation. What is the state and federal tax that I would incur on this amount if I made $12,000 on 1099 Misc.

1099-misc income: You are self employed or independent contractor. You will report your income and expenses on schedule C or C-EZ (Form 1040). Then you put net income (or loss) on line 12 of Form 1040.

In your case the ncome is not subject to SE tax at 15.3% so you do not do schedule SE.
Read: Your U.S. Tax Return: Tax Filing by Self Employed Sole Proprietor or Independent Contractor