Yamaha 4s tend to clunk pretty good when moving in and out of gear. Probably normal. I assume you have a F150 or F200 engine on your 2120. Next time you are idling and feel/sense the vibration put your tabs down all the way to create some drag. If the vibration decreases or goes away then what you have is likely PROP CHATTER which is considered normal. Prop chatter occurs when the drive train is intermittently under load. Pushing, not pushing, pushing, not pushing and so forth. The vibration is not actally coming from the prop, but instead is a symptom of the drive train. I had an f225 that did the same thing.
That's my best guess based on the info in your post.
jim