I would think your CV joints would have to be pretty well destroyed to make the clunking sound you've been hearing. Whether or not they're worn enough to replace as opposed to just replacing the boot is hard to tell from here. They really should be removed, cleaned, and inspected. I would think it more likely that one or more of the rear suspension strut bushings have worn out (which would normally cause a squirrely feeling in the rear end when shifting or getting on or off the gas but could conceivably cause some noise, or the differential rubber mounts have worn allowing the diff to move when shifting or changing to reverse. What's the model, year and mileage of the car?