Hmm, first, a word about fölött. Like English works with prepositions (above the city), Hungarian mostly uses postpositions (and suffixes) instead (a város fölött), so those always have their respective relation to the noun appearing before them.
Now, "What is the city above?" can have two meanings in English. If you're wondering about that city up in the sky, you could ask "Mi az a város fent?" The fent here is not a postposition, but a location, it's not above something, but just above. On the other hand, if you want to know above what the city is (where you also could ask "what's below the city?"), you simply go with "Mi fölött van a város?" Here's the postposition fölött again, making the corresponding English question better as "Above what is the city?"
Ah, right, thank you. That needs some fixing.
I intended to go for a more literal "What is the city?", basically asking for the name/identification of that city. I thought that something like "Mi az a város?" could work, but maybe it doesn't work that literally in Hungarian. Maybe something like "Melyik város az (a fent)?"