Is your wife an employee (she gets a W-2) or is she an independent contractor (she gets a 1099-NEC)? If she is an employee, boxes 15, 16, and 17 of her W-2 should be blank. It should not show any New York wages or New York tax.
If she is an independent contractor, probably the only useful documentation would be a letter from the client saying that she never worked in New York.
The IRS will not audit your state tax. In the unlikely event that New York audits you, Audit Defense should help you with the state audit.
