I use a standard PS2 controller hooked through a USB adapter that I got from RadioShack. It works like a dream. In fact, when I started playing this game for the very first time, I thought "Hey, this is a PS2 game.... I bet it would work fine with a controller on PC" and haven't stopped using one since.
Well.... except for the year and a half that I wasn't playing the game. Dur.
How did you hook the PS3 controller up to your pc? I have no experience with that controller, so I don't know if outright hooking it up through a usb port will make it work. There are always workarounds to make it work over bluetooth, but you'd need a BT adapter for that and then some external program to make it all work. Something like that. I tried it, didn't work, I stopped trying and went back to the wired PS2 controller.
Is your logitech controller (silly question, I'm just making the rounds) usb as well? Vista should just see it as a game device of sorts and since you can change the gamepad configuration outside of ffxi, do the cursors move in the little test areas when you try to configure it? It'd be really odd for the config program to register the inputs, but not ffxi. You said you went to the playonline viewer config, but did you use the "FINAL FANTASY XI config" program?
I fully advocate using a controller to play the game. Completely. Of course, there's nothing wrong with keyboard controls. Figure out what's best for you.