Interesting question, so I had a run through the holdings of the ZAA zoos from the last census (as of Dec 2013). I may have missed a few, and it will probably be slightly different now anyway, so don't take the following as 100% correct. While I was looking I couldn't remember if the question was about marsupials in general or just macropods, so I counted for both.
The collections with the most marsupial species were Healesville and Perth, both with 26 species. Of those there were 10 species of macropod at Healesville and 9 at Perth. Going down in total from there were Halls Gap with 24 species (12 being macropods), Australia Walkabout Wildlife Park and Currumbin with 21 species each (12 and 9 macropods respectively), Cleland and Taronga with 20 each (9 and 8 macropods respectively), and Adelaide with 19 species (10 macropods). Melbourne was way behind the other three major city zoos, with only 13 species (6 macropods). The Australian Reptile Park only had 9 marsupial species (6 macropods).
All species are native except the Matschie's Tree Kangaroos at Adelaide and the Goodfellow's Tree Kangaroos at several places.