I did this recently and has worked perfectly to stop window whistling (I am assumming you are talking about the vent window).  I put a very thin bead of clear silcone sealant on the edge of the black rubber (you could use black colored sealant if you wanted) just where the window touches the rubber.  let it dry without the window being closed to touch the sealant.  once dried close the window which should be a little more snug than before.  Works like a charm.  Now I can hear the radio a little better and the person next to me (I have an air cooled westy too so it is still a little loud inside).

I the main window is whistling then new rubber is probably the solution

tim