If you get it out of the water, look both from underneath, and open up the reverse gate and examine from behind with a good flashlight. Even a tiny piece of hard wood between the housing and the impeller can cause a problem.
If that fails and you are sure there is still something in there, then you need to pull the pump off. This sounds like a daunting things to do, and I thought so too until I did it for the first time. It is EASY. On a Yamaha it involves the removal of 5 bolts and one clip fitting. The only challenge some have had is if the shaft is stuck.....mine wasn't and came out easily. This may be more of an issue for salt water boaters???
Here are some links to threads that discuss this problem for Yamahas
Boat test video explaining the pump system
How to dis-assemble Jet pump video, and photos
- I think I have something stuck in the impeller
- Easy trick on how to clear debris from your intake while on the water
- Damaged impeller linings
- Golf ball stuck in impeller!
- Photos of stuff stuck in impellers
- How to clear your intake grate