With SSL it’s a bit of a mess involving CA certificates and other things. After you have the PKI in place you also need to configure your services to use the PKI for authentication instead of its internal password database; this is a nightmare on some services and a piece of cake on others. It also means you need to go to the hassle of signing all of your user’s keys so they can log in with them.
Most competent users can grok SSH keys in no time but it takes a bit longer to get their heads around SSL keys (the extra CA certs and key certs confused me when I first discovered it).
Pick what’s supportable. SSH+SFTP is great for Unix people, but FTP over SSL is probably easier to do if your users are Windows-based and are pretty clueless about anything other than Internet Exploiter (and you don’t mind risking that your users will choose insecure passwords).