In terms of prestige, drbuff is correct that it's usually the federal government. In addition, if you're thinking about going into BigLaw, there's much more of a likelihood that your experience with the federal court will be more relevant to your practice. In state court you'll deal mostly with things like DUI, domestic violence, and other similar crimes.
Although on the flip side, precisely because it's likely underfunded, you'll get more hands-on experience in state court. You'll probably handle full cases and be the point person for client contact, plea negotiations, etc.
So it just depends on what you're looking for. Please feel free to PM me for more information.