Istanbul is actually a relatively diverse city, religiously, both currently and throughout its history. Even though it was the seat of the Islamic Caliphate for nearly 400 years, the city always had thriving communities of non-muslims. Due to its size and importance, Istanbul also had a great deal of history that remained influential as it was never conquered and destroyed the way that Isfahan was in the 18th century which actually caused the capital status of the city to be moved to Tehran.
Isfahan is also slightly less diverse, particularly now, perhaps because of its location within the more homogeneous region of Iran and in the midst of a non-secular culture. The influence of Islam is huge in the city, perhaps evidenced by the massive and beautiful mosques in the city.