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According to the NYS Department of Taxation and Finance, auto body repair work is taxable for both the labor and parts charges. See this link to its site: http://goo.gl/0jsan8
The people that have told you that only the parts are taxable are probably thinking of improvements or repairs to real property, where only the parts are taxable. If you tint the windows in a house or other building, only the materials would then be taxable.
I hope this answers your question. Please let me know if I can clarify anything or answer any additional questions. Thanks, Jonathan
Here is a link to a question asked of the NYS Dept of Taxation and Finance: http://goo.gl/1KvJmc. In this case the business was applying film to windows that made them stronger. However, in this case the department stated that unless the film was applied as part of a replacement of the window, the application of the film would not be considered an "improvement." Furthermore, the rule that makes labor charges for "improvements" exempt from tax is when they are done to real property, houses and other buildings. A automobile is personal property so the exemption for improvements would not actually apply at all.