Waiting until after dark and turning off all lights in the room will help keep reflection down. Try to keep the camera at 90 degree angles from the front of the glass surface. I have a 72 bow and sometimes it's difficult to photograph through the front glass. You can also use a clear container from the kitchen to break the surface of the water in order to shoot from above. Use a tripod if at all possible.
Like HUNT said, turning off your pumps, eliminating water (and coral) movement, will help with blurred images.