You need to isolate the noise. Is it coming from the engine or the pump assembly?
What are your idle RPMs? On some of those older skis, there is play and vibration in the impeller. Manufacturers started putting in different anti-vibration cones in the late 90s to stop the tick or rattle. If your idle RPMs are too low, the rattle gets louder.
Regardless, it may be time to go through the carb. Low idle rpms could be a sign of a loss of fuel in the idle circuit. A tick or a knock in the engine could be a sign of a lean condition. With a 21 year old ski, it might be time to rebuild those.
You may also try searching over at greenhulk, very large forum over there dedicated to PWCs