You may remember that I had posted about setting up a remote file server (via the web interface), a little while ago. Well I just stumbled across this post which talks about using secure FTP via the ssh tunnel. It’s dead simple to setup and is actually quite an elegant solution. It does require FTP software that supports SFTP, so it’s not quite as user friendly or configurable, but it’s great for power-users. I think I audibly said, “duh!” when I stumbled upon this. Also, it’s nice having the SSH capability exposed externally. Note that the tutorial is for FreeNAS 8, but is totally applicable to FreeNAS 7 (if you’re like me an are sticking to the legacy server software).
And regarding security, I would definitely use a different port than the standard SSH port, at least externally. Otherwise you’ll get clobbered with traffic from hackers attempting to connect to your server for not so nice reasons. You may want to consider using a keyfile as well – which makes it less convenient, but much more secure.