Water disturbance from the pontoons can also cause it on some toons.
Pontoon boat motor cavitation. There is virtually no headroom in trimming the engine while underway. Its a plague of pontoon boats and why merc invented Big Foot motors. Secondly it causes those vibrations which makes your ride less comfortable.
Standard props are pitched too steep for the slow speeds 20-25mph at full throttleand they run on the edge of cavitation. A damaged prop can also cause cavitation which you will feel in the form of vibration. What are the Standard Shaft Sizes.
A similar but quite separate issue is ventilation which takes place when air is introduced to water around or to the water flow fed to a propeller. They arent the same thing and people often mistake one for the other. If you can post some pictures of the relationship between the lower unit Cavitation plate in particular and logs.
Gas bubbles then condense elsewhere on the blade releasing energy that causes metal erosion or cavitation burn. First it can physically damage the propeller. And will try to post them up.
Water disturbance from the pontoons can also cause it on some toons. It has a top speed of approximately 36 mph at 5600 rpm or so with 4 person load. If youre experiencing a less than perfect ride you may want to check on your propeller it could be the main cause.
They keep water down at your prop and intake improving water pressure. This is when the propeller intermittently pulls out of the water when underway hurting your boating or fishing experience. I am by no means and expert and I am sure more people will chime in here but it is my limited experience and knowledge that the main cavitation plate on the outboard motor has to be level with the bottom most portion of the transom it is mounted on.