First, he can't legally make that type of deduction from your paycheck without your written consent.
Second, he has to pay you your final wages plus accrued but unused vacation by the next regularly scheduled payday. If he does not pay in full on that day, you have a claim and should contact the Illinois DOL and talk to an Illinois lawyer. Sometimes the statutes of limitations for these kind of things can be short and contacting the DOL may or may not stop the running of the limitations period.
Third, go ahead and file for unemployment. Normally, quitting would preclude you from getting benefits, but this situation could be an exception. In any event the unemployment system is very employee friendly, so you've got a decent shot.
Good luck!