You can advertise in your site that if a customer would like to order with tax exemption that they should contact you. They would provide the tax id so you can verify it, and then mark their account (or set them up with an account and mark it) with the status.
This way when they go to login next time they will not be charged tax. It is a common practice.
Or you can simply go to Admin > Site > [Site Name] > User Management > Site Users > Edit Site User > Scroll down where you see Additional Information and check the box that says Tax Exempt.
By doing so the user will not be charged any tax one they logs in to the site and places an order.