You will need to remove the black stains by sanding and then restain and apply a good clear finish.

Use low-tack masking tape, blue painters tape, on the glass before doing any sanding. This will protect the glass from scratches. Also try to use sanding blocks (sanding sponges) instead of sand paper. The blocks are easier to control.

If the black stains still are present after sanding then a wood bleach will have to be used to get back to a neutral color. Another option is to sand most of the stains out then restain with a darker or richer color to hide the black. Of course this means refinishing all of your windows to match the new color.

After staining use McClosky's marine spar varnish (Man-O-War) as the clear protective finish. This is great stuff and does a better job than most clears on the market.

If refinishing isn't to your liking then you can paint your windows. This will also be a lot work. Personally, I think refinishing is easier.