I have the same issue. I've got a really good yard mechanic who advised, over the phone because we were underway, to check for spark for each piston and oil level which was ok. First I found that one plug wire had fallen off, and felt it was time for tune up so changed all the plugs and wires, although gapped them at .035" as suggested by marine store, although then checked the engine guide which said they're supposed to be gapped at .045" . I'll get to it this weekend and report back if it decreases clunk noise. At rpms higher than idle, it sounds fine in or out of gear.
10-6-2015 update: your issue could be bad springs on your damper plate between the engine and transmission. After a seizure of my port engine, we inspected under the oil pan and found a piston bracket that came loose off of the crank shaft had pounded through the pan. Rebuilt block underway.