SSH, definitely. You can transfer files if you need to via the "scp" or "sftp" systems. I would advise against ftp or telnet, as they are clear-text and leave nothing to potential snoopers' imaginations
You could also try one of the web-based administration tools (like "Webmin"), but I've never really played with those. I haven't run into a problem yet that wasn't best solved (speed ans server impact) through a text-based terminal..