New Orleans and some small areas in the area around it could develop in this fashion. Perhaps the Spanish keep the city and a series of treaties leads to the city becoming an area split into many different parts with Spanish, British, American and French areas of control. Eventually the city then is united and made into a city state that focuses on trade between the US, Caribbean, whatever power owns Basse Louisiane and Mexico.
Zanzibar is a city that when connected or in control over the various island strings off the coast of the Kilwani sultanate could meet this requirement. Zanzibar has one major weakness abd that is that for the most part, the city was based upon the slave trade. Thus it may be necessary to change its mode of trade or keep European societies far more conservative and lax on the issue of slavery.
Many of the cities along the West African coast. Somehow restrict European power projection in the region and make the slave trade remain longer outside Brazil and Africa.
Musqat. For most of its history, Musqat was a city state that was seperated from the states of the Omani interior. It could remain so quite easily. In the future though, it is conceivable to imagine major demographic changes wherein the city is majority non Arab. Such challenges would need to be addressed, as well as the dangerous tribes of the interior and the powerful states in Iran.
Numerous cities along the coast of Hindustan.
Baghdad for much of the Saljuq period operates as a city state under the Abbasid Caliphate. If you can keep the Abbasid in Power in Baghdad, but also weakened enough to not make a resurgence, then in modern times, a monarchy in Baghdad could rule the city as a city state. The same goes for Samarra, which according to some accounts had reached over 100k inhabitants during its period as the capital of dar al-Islam (Abbasid Caliphate).
Keep the Holy Roman Empire seperated constantly, then you perhaps could have numerous city states. This might also require no reformation.
Etc... I can perhaps decide on more at a later time.