Sort answer: I would suggest you put down the person who was your manager.
Long answer: If they call for a reference and ask for your manager, then the answer is they no longer work here, and (maybe) here is a number you can reach them at. If they call and ask the new manager about you, it won't do you much good because the new manager cannot be a reference. They could say that they never worked with you or they could say they've never heard of you. If the second happens, then your potential employers have to verify that you are not lying on your application