Sri Adi-Sankaracharya's commentaries on the Upanishads are most popular in present time. Are there any Gaudiya Vaishnava commentaries available on the Upanishads?
Well, I do know of a commentary on the Katha Upanishad, authored by Swami B.V. Giri, which adheres to Achintya-Bheda-Abheda. Unfortunately, the book is not available online. You can buy it here.
Edit 1: I found commentaries written by Sri Bhakti Prajnan Yati Maharaj free online on the Taittirya Upanishad, Aitareya Upanishad and Chandogya Upanishad. You can read them here.
Also, you might be able to purchase all the twelve Upanishadic commentaries authored by Sri Bhakti Prajnan Yati Maharaj here.
Edit 2: You can also read Baladeva Vidyabhusana's commentary on the Isha Upanishad free in Hindi here. By the way, Baladeva Vidyabhusana also wrote commentaries on other Upanishads but none of them survived.
Edit 3: You can also read A.C. Bhaktivedanta Swami Prabhupada's commentary on the Isha Upanishad here.
Edit 4: I found all the Upanishadic commentaries of Sri Bhakti Prajnan Yati Maharaj online. You can read it here.