If the motor mounts are good, I'd agree with Don Long.........probably something in the pump. It could be very small. I had a small piece of plastic bag in there once that made mine vibrate like crazy. You may have to remove the intake grate to see. It is also possible to have a small ding in the impeller that would imbalance it enough to cause vibration.
One other thought is a fouled spark plug. I've seen 1 fouled plug do very weird things on these skis include causing vibration, and you often will not see the problem except at higher rpms. My general rule of thumb is to replace the plugs on any Yamaha 4 stroke at the first sign of any problem, since this is so common on these skis.