PCI is way faster. With USB, you can typically only record 2 channels at a time. There are a handful of exceptions, but I haven't heard anyone raving about em. PCI interfaces will allow you to record as many channels at once as you want, for all practical purposes.
Firewire would be the way to go imo, there's a ton of great fw interfaces out there. You could use the PCI slot for a firewire card if you don't have a firewire port. Then you could hook up your video camera, external hard drives, all kinds of other fun things too!