I do not know much about any pollution checking center for vehicles in Vrindavan, but yes, at a petrol pump, Junction Road, Sonkh Adda, Mathura, there is a Pollution Checking Center where one can obtain an emission check certificate, also known as a Pollution Under Control (PUC) certificate.
If not, Hodal (Palwal, Haryana) approx. 30+ km from Vrindavan on National Highway 2 on the left side (after crossing the Uttar Pradesh border), there is a petrol pump with a 24-hour open Pollution Under Control Center.
I received an emission check certificate for the motorcycle at Hodal, Haryana.