I do not know much about Vrindavan but yes, at a petrol pump, Junction Road, Sonkh Adda, Mathura there is a center where one can obtain an emission check certificate also known as 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 24 hours open Pollution Under Control Center.

I received an emission check certificate for the motorcycle at Hodal, Haryana.