Assuming this is happening when in gear, I'd be thinking something in the drivetrain, including engine mounts, as someone else suggested. If it happens even when not in gear, engine mounts would be #1. I had a thumping noise when in gear after installation of new shaft and new cutlass. Turned out the shaft wasn't true--the wobble caused the thumping sound. I would bet that a bad cutlass bearing would do similar.
2000 Beneteau 331
Northern Chesapeake Bay
Ambition is a poor excuse for not having enough sense to be lazy ~ Steven Wright