The only thing I know of that wipes out mildew is bleach or other chlorine-based chemicals (the stuff you use to remove mildew from bathroom tiles). I don't know what it will do to neoprene, however. You may want to try it on a small area to see if it dissolves the rubber before wiping down the whole boot.
Of course, you could hang one of those Christmas tree air fresheners in each boot when not in use ;-)...
-bd