There is no "best" way, it depends on the floppies and what you are trying to achieve. Assuming that 1) the disks don't have copy protection 2) you want to create simple image files readable by most other software 3) using a tool that runs on old windows or DOS,

basically any disk imaging utility will do the job. I can suggest DskImage (http://www.brutman.com/DskImage/) which has persistence options for reading worn-out disks, or even FreeDOS' diskcopy which is super simple (diskcopy a: example.img) .