As a first step, I'd recommend replacing the spark plugs. A bad plug can cause all types of running problems on these skis. I highly recommend this as a first step with any Yamaha 4 stroke when there is an issue with loss of power. New plugs will fix 95% of the problems.
If you try new plugs and still have a problem, I'd suspect a dirty fuel injector. As a first step get a bottle of Yamaha Ring Free Plus, and run it through with a fresh tank of fuel. I'd double the dose (use 2 oz./10 gal. fuel) to see if this will fix the problem. If it is still running bad after this, you may need to remove and manually clean the fuel injectors (they have a screen filter that occasionally gets clogged).