Every morning when I wake up my lower back, shoulders, knees and ankles are achey. What could be causing this?

Arthritis. Without knowing more about your age and medical history, a "best guess" would be that you are suffering from some form of arthritis. I would suggest that you make an appointment to see your doctor right away to get this checked out.
Many joints hurt. Many possibilities. Because so many joints are involved this may be an illness. You should see your doctor for an examination to find out the cause and then proper treatment can be given.
Many things. These symptoms could be caused by, literally, hundreds of diseases and syndromes across many areas of medicine. You should start with seeing your primary care physician who could diagnose or at least narrow down the possibilities with a good history, examination and possibly x-rays and labs.