Well, depending on the USB chipset and version (1, 2 or the latest, 3) the data transfers can take a serious chunk away of the available CPU processing power. Firewire has less troubles with that, but can be less compatible with other software solutions.
My best advice is to purchase an external drive like the WD MyBook Mirror Edition (automatic backup!) and transfer all the necessary files from that external drive to your computer. After processing the files, copy them back. This way you do not require the external device constantly and have a 2 way backup as well.