Unless you have proof, do NOT have this conversation. You need to either have the "I know all about you and _______, and I won't live in an open marriage" talk, or nothing at all. To play it down the middle, and accuse without iron-clad proof, only makes you look weak, needy and defensive.
I would agree that it appears highly likely that your wife is having at least an EA with this man, and she is disprespecting her marriage and acting inappropriately. I would recommend you either:
1. Get iron-clad proof and confront her; or
2. Just assume she is (having an affair with her boss).
Playing it down the middle is a recipe for disaster.