Is it a 2 or 4 stroke? If 2 stroke, try running some Seafoam through the engine. Get a gallon gas can, put in gas, oil (if premix), and a can of Seafoam. Hook this directly up to your engine, bypassing the filter. Run it for about ten minutes at idle, then let it sit for ten minutes. Keep doing this until the gallon of gas is gone.
Your boat will smoke like crazy as the carbon deposits are burned off, but it should run much smoother afterward. I did this on my old boat every year, and the difference before and after was always impressive. You can see a lot of videos on this on Youtube.
I would also check your plugs, carbs, if your mix is too rich, etc. There are a lot of things that may be hindering your performance, but the Seafoam is a quick way to check one area off of the list. Even if it is not carbon deposits causing the issue, your motor will be much cleaner, which is always a good thing.
