A buddy of mine just went through this on his sailboat. There are 2 ways to handle this. 1. Remove the windows and take them to a place that can strip, re-anodize and powder coat them. It's not gonna be cheap but it is a fix that will probably outlast the rest of the boat. 2. Paint them yourself. Probably a more realistic fix. As an old aircraft mechanic, I've probably painted more aluminum than most. Like any paint job prep is 90% of the job. The old paint can be stripped with either a good chemical stripper or the best way is to have them plastic media blasted. Then the parts need to be etched with a phosphoric acid etch ( should be available at any good sized paint supply). Then apply a prduct called Alodine ( dupont) this provides a protective layer of artificial corrosion to the aluminum surface and helps the primer stick. Finally any good epoxy based primer followed by the topcoat. Check with the local airport, there is probably someone around that can steer you to the local sources for the materials and give a bit more detailed advice. or e-mail me and I will go into more detail without taking up too much space here. Good luck with the job!
Norm