Of the ones mentioned my favorites are:
*Zanzibar
*Kilwa Kisiwan. Or any Swahili city state or federation of them.
*Mogadishu
I don't see people considering:
* Hausa city-states
*Tripoli. Trading center between the Mediterranean and the interior of Sahara
*The capital city of the Kanem–Bornu Empire. It can fancy all the territorial claims it can think of but it mostly consists of sand and nomads.
*Maya city-states. (kinda of difficult with Spanish conquest, but one can have dreams)
*Other Mesoamerican city-states.
*Central Asian cities along the silk route
*Russian city states: Novgorod and Pskov. The Venices of the North!!!
*Malacca in the middle of Strait of the same name. If things had worked another way and the Dutch or British had more foresight it could have been Singapore's twin.
*Brunei
A good source of information and ideas of city states is:
Mogens Herman Hansen (ed.) 2000.
A comparative study of thirty city-state cultures 2000.
ISBN 87-7876-177-8.