I believe recent versions of WinUAE can read Amiga drives directly. So you should just be able to connect it to your PC (probably need a 2.5"->3.5" kit) and then back it up to another drive under UAE (which could be a hardfile or a subdirectory on your PC's drive.
I've never actually done this myself, though, but at least a few here have. They can probably give you more detailed instructions.
