Brad,

           I cannot speak at all to accessibility, since I've never had a client with a need for FTP capability, but you should definitely give Filezilla a try to see if it plays well with JAWS.  It's a great little FTP client, and if it does play well with JAWS I'll bet you'll love it.  It's free and open-source, so there's no risk in trying it and it's been around for a very, very long time.

Brian