I do not know what the problem is but
1. air leaks can cause much more noise than without the leak. So check the tubing, maybe cut an inch off the ends near the pump and see if that helps.
2. the back flow valves can partially fail causing more noise. These are usually flat pieces of rubber held fast over the inlet and outlet of the diaphragm. THese can fail due to dust, dirt, accululated oil that dries out. So you might try replacing them, or you might try cleaning them, or you could add a few drops of silicon oil to these locations and see what happens.
3. higher back pressure on the pump causes more noise than lower back pressure. Perhaps the air stone or filter you are pumping air to has become plugged. Replace the stone or clean out the air line at the filter and see if that helps.
4. buy a new pump. I really think the ones designed for deeper water, and they will be advertized as such, work well and silently.
Frank