There's a few different ways to clean an immersion circulator.
To remove the mineral buildup they suggest "Depending on use and water hardness, scale and mineral build-up may occur. Clean by filling a pot with a solution of vinegar and water and running the circulator for about 30 minutes."
I've also heard that using the CLR cleaner on it works great as well.
For de-contamination type cleaning they suggest using an bleach wash, then vinegar wash, then alcohol wash. One thing to remember is that if you bag your food before you put it into the water bath there probably isn't anything in the water that could make it through the plastic.
There's more good discussion on cleaning an immersion circulator here:
Cooking Issues
Here's a link to a video about generally cleaning an immersion circulator:
http://www.metacafe.com/watch/2157295/how_to_clean_a_polyscience_7306_thermal_circulator/
Sorry that it's mainly links and not a "here's how to do it" but there seems to be differing ideas on how to do it best and I figure you're better able to make up your mind for what you personally feel comfortable with. Hope this helps!
Thanks and happy sous viding!
Jason