Trust your instincts... If you think she's cheating then stand your ground. If this guy was smug to you it is very likely he is...
How close is this female friend to your wife? Would she lie to you to cover up your wife's affair? If not, then ask her roomate directly if her roomate is sleepign with this man... Often people will perform a passive lie (that is, turn the otherway) for a friend, but often will draw the line at an active one (directly and knowingly offering incorrect or incomplete information).
What you were doing is not creepy, you are protecting your son. That's not creepy, its called parenting. You have a right to know who is staying in the home that your son is staying it.. It's called being a good parent.
Creepy is handing your son off to an estranged wife and NOT bothering to follow up to find out where your son is, or who else is in that home at the time.
Have you done any research on infidelity?
It is an addiction... the best route to end it from what I read here and in formal textbooks from experts is to EXPOSE the infidelity to the public (friends, relatives, workmates), particularly on the OP's side instead of your wife since you want your wife supporting you long term?
Do the resarch. There's a great text book called "Not Just Friends" by Shirley Glass... Glass pretty much bursts the "friends" bubble inside of just a few pages.
Your first step is collect as much intel as you can and based on the intel if there is an affair going on, expose the affair to the OP,s workplace in an attempt to publically shame him away from your wife.
You will have to gauge your relationsihp with your In laws before exposing the infidelity to her friends or family... that is a dice roll and may do more harm than good.
