I have a Firewire hard drive and recommend Firewire. However, I'm starting to get concerned about the future of Firewire, considering most new consumer DV cameras appear to have USB 2.0 connections??! And with Apple moving the iPod to strictly USB 2.0 only I'm starting to get concerned that even the maker is abandoning it! Also, you'd expect at least the 12" PB to start shipping with FW800 by now.
FW400 is slightly slower than USB 2.0 in theoretical max transfer speed but makes up for it through a faster sustained average transfer speed and I don't think this degrades with distance of cable, unlike USB 2.0. That said, I feel that the proliferation of USB 2.0, the acceptance of it as a standard by Apple, and by the refusal of PC manufacturers to feature Firewire as standard on all computers makes its future still a little sketchy.
But I would still go with Firewire.