My best recommendation is to call the physician who treats your son's allergies. If it's a Primary Care provider (Pediatrician/Family Practitioner), I'd call a local allergist/pulmonologist to see if they have any recommendations.
As far as the validity of the issues with a humidifier, I'd certainly look into how likely it is to have an issue with a humidifier and toxicity. Molds love warm, dark, damp places. So, humidifiers make a perfect breeding ground.
The humidifier you purchase should come with cleaning instructions - they may recommend bleach, or they may recommend other products to prevent growth of mold/mildew. It appears many newer humidifiers are now treated with Microban technologies to help prevent the growth of mold/mildew.
I'd recommend reading the section of this link called "Disadvantages and Risks" and then use a site like WebMD, GoogleHealth, etc. to verify the commonality:
http://en.wikipedia.org/wiki/Humidifier