I second JesseLyon2002's suggestion. Duragloss Nu-Glass has been the only thing I've found that works for bad waterspots on glass. My car had bad waterspots when I bought it, and I fought them for awhile. Tried scouring pads, every window cleaner, vinegar, and some paint polishes. A local glass shop recommended the Duragloss, and tried a test spot for me. Took them off immediately, so I bought the bottle. It can be used by hand, but a PC makes it almost effortless. It can be found at a lot of glass specialty shops, or online. A little bit goes a long way, so a small bottle will last awhile.
Dave