There is a property in Mirboo Noth call Campbell Homestead they are a farm stay, can't remember what sort of activites you're able to do there but I can tell you they can book WAY in advance.

There is a childrens farm in Collingwood I think, not sure about accessibility transport wise but its an inner city suburb.

There is the Aquarium, Luna Park, Science works in Spotswood (I think you can take a ferry/boat trip there from inner Melbourne) the Zoo ....... That is all I can think of