Go over it 3 or 4 times with glass cleaner and keep turnign the cloth, then a thin, and I mean THIN polish with some AG glass polish, will look top notch after that.

I find that the windows on my shitter mondeo look great then you roll them down and back up and they smear. Only way to sort it really is to take glass out, clean the bit you cant get to, and all the seals at the same time.