I used to live on a custom-built houseboat. In my state (California), houseboats are appraised by marine surveyors, as Neil said. And, Joe is right, too - they are considered (and taxed) as personal property - but appraised as boats by qualified marine surveyors.
There is a difference between a houseboat (which is self-propelled) and a floating home (which cannot move about under its own power - has to be towed). I'm not sure who appraises floating homes, but I would guess marine surveyors. Part of the appraisal process is a thorough check of the quality and condition of the flotation, and I doubt that many personal property or real property appraisers are qualified to do that type of work.
I was just bouncing around http://www.boats.com and see they have N.A.D.A. Appraisals online, minimal info but it does give prices. It's not on the opening page, just do a search for a boat and it should be listed in the left hand column of the search results page.