Tread very carefully. Most people are sensitive to these issues and considering how small your company is this could ruin your relationship with your boss.
The wife is possibly your best shot. If you can trust the wife to keep your secret, bring the issue up with her. Ask her to bring it up with boss man while keeping you out of it. She can just mention "there have been complaints" or something similar. One has to assume there might be a similar situation at home which has been going on for a while, so this approach may have limited efficacy.
You may not have HR, but someone must be managing the office - buying supplies, cleaning, managing the shared areas. Go to that person and state that the bathroom is too dirty to use and it needs to be cleaned more frequently. Don't mention your boss or anything else. Simply stating the facts removes the "personal" element. A situation exists that is hindering your ability to work effectively and it needs to be rectified. It doesn't matter who, why, or how.