I vote for confronting Dad. Let him make the decision to either stop his affair or tell your mom.
I know people always say "Oh, she (the wife) MUST have known, she was probably ok with things the way they were." I don't agree for a minute. Most of us here were blindsided by our spouses affairs. Even when it should have been obvious, you just don't think YOUR spouse is going to do that to you.
Seems the best possible outcome would be if he is embarrassed and/or shocked to be found out, and decides to stop the affair on his own. Then your mom is spared knowing, the family can remain intact - although YOU are still stuck with the burden of knowing. Still, you would probably have some respect for your dad if he reacted that way.
If you confront him and it blows things up - as in, he decides to tell your mom and run off with OW - well, that is probably what would have happened anyway, wouldn't be caused by you finding out. And your mom has a right to know she's being exposed to sexually transmitted disease etc.
And creepy though this sounds, before you confront him, you might want to accumulate a little hard evidence - both to break through HIS inevitable denial, and it may be useful for your mom later.
So, so sorry you are stuck with this information. But it doesn't seem like just pretending it doesn't exist is much of an option - leaves a huge burden on you.