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Jack the bike up on a lift and spin the wheel slowly by hand and listen closely all aorund should be able to narrow it down that way and see if it is coming from the case or the wheel.
'05 Fatboy started making this weird knock with every 1/2 rotation of rear wheel. In my case, the sprocket side bearing was teeter-tottering in its seat and had mushroomed the spacer slightly....drove my local tech guy crazy looking for the source!
I'd swapped out my original solid wheels for chromed ones last year (new bearings installed then), had noticed a weird "ping!" from the rear sometimes when I'd put weight on it, just sitting there, but not all the time....was totally fine otherwise. Almost exactly a year later, we were riding 2 up about an hour at highway speed, exited for gas when we noticed the steady knock at low speed.
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