There are too many kids involved to blow this thing out of the water over a past history, suspician that somethings going on, and a emotional relationship.
Please tell the boss's wife ASAP. Even if there is no physical affair going on at the present (which I don't believe for a minute), the past history and continuing emotional relationship is more than enough to call his wife. When I called the OW's husband to expose, I was sick to my stomach wondering if I was doing the right thing but it is essential and thank God I did. The OMW deserves to know what has been going on behind her back for YEARS. Perhaps she is already suspect about her husband but chalks it up to being a jealous wife. I didn't have hard proof when I exposed and knew the husband would have to take my word for it that our spouses were involved in an affair. He believed me without question and even thanked me for contacting him since he was suspect but had nothing to go on other than suspicion. The fact that you would contact her to tell her this would be a giant red flag for her. Should she chose to ignore it for whatever reason, that's up to her, but at least you told the truth.
None of us knows what goes on in the wife's house but she deserves to know the truth for her sake as well as her children's. No offense, but you seem more concerned about your wife losing a possible bonus check and/or people thinking you are a liar than you are about doing the right thing. If you plan to divorce your wife, why do you care about her job? She doesn't seem to care about you, her own child, or other people. I understand you care about her son and don't wish harm on the OM's family but your wife and the OM have caused the harm not you. The fact that your wife is using her relationship with her boss as finanical leverage makes her sound like another kind of "working girl."
Sorry you find yourself in this situation, but you are allowing it to continue.