I use firewire (800) for my Time Machine backups. Mainly because my 1.5tb Seagate drive has is and I am not using that port on my iMac for anything else.
Like the other 2 have already said, it won't be bad either way. But, if it was me i would just go with the firewire. If you ever had to use the drive for something else in the future it will already be set for better speeds.