Normally we use white vinegar and just run a pot of it through followed by several pots of plain water, but the only vinegar in the house right now is red wine vinegar, and I don't think that will work well.

Anybody know of anything else I can do?

A mixture of baking soda and water works at about a 1-4 ratio.

I've heard that just boiling water in it will kill the bacteria

Just keep it filled up with coffee constantly! That's what we do at home!

I usually run vinegar thru the machine and then run water thru it to get all the vinegar out. Now with the pot itself, I use CLR and then rinse it out really, really well. I love CLR, it has a lot of good uses.

My brain wasn't working and I was about to say "Drink the coffee" XDDDD