Typically, you won't notice much of a difference between the two as far as transfer speeds. If you have the option, certainly go with 1394B then 1394A then USB2 and way behind that and almost not considered at all is USB1.0. Another aspect to keep in mind is that doing heavy work on a USB2 drive can make your CPU less responsive to other things, as utilization can be anywhere from 5% - 60%. Firewire (1394) is much lower in that regard, topping out at around 10% I believe.
USB is more software controlled and relies on burst speeds. Firewire is a bit more dedicated and you'll see better sustained transfer rates. That's why people say for a bunch of small files, USB2 can have the edge, whereas if you're working with large files like video content, Firewire is your friend.