How do I get layers of cracked paint from windows?

First with a house that old, I would test for lead paint. You can buy an inexpensive kit at any hardware or home store. Then if its not lead paint you can either strip it with paint stripper, if its fume free you want try Citristrip - be sure to not let it dry out, I put some plastic wrap over it myself. If something stronger is needed I like Kleen-Strip be sure to wear rubber gloves and keep it well ventilated.

If it is lead, then I personally would have it done by professional remediation company.

Citristrip Stripper. Lots of scraping and sanding.

Don't use a heat gun, will crack your glass. We took out our windows and took them to a stripping co. Also took our trim and baseboards. Did a room at a time as we could afford

Note! beware of lead paint! In a structure this old, that may be an issue -- and will require special equipment or a professional.

If you don't want to be bothered with all the stripping , sanding, etc., would you consider having a carpenter make you new sills? Even if you want to paint them, a carpenter may be able to obtain pre primed ones for you. Priming and painting or staining new sills may be less time consuming and less costly.