You are processing your mouse movements in a script. NGUI processes mouse movements too. You want to know in your mouse movement code if NGUI has processed the mouse movement. Use Unity script evaluation order to ensure your code gets processed later than Update meaning your code will be evaluated after NGUI. Now you only need to attach a script to your NGUI widget, object, background, whatever, that sets a public static bool to true in an NGUI Event like OnPress. So your attached script would have an event listener for OnPress in Awake, and a method that sets a public static bool to true if the bool passed to you from OnPress is true, or you could use OnHover or OnDrag or whatever best suits your needs. Then in your mouse movement code you can check the value of the public static bool and respond accordingly. Don't forget to reset the bool back to false!
The NGUI code is adequately documented. Check out UICamera for events you can listen for.