i was watching a japanese tv show once, and apparently, you could get some of the best tuna in japan (as well as numbers of other fish) if you go deep into chiba, btw. i'd love to try this for myself one of these days.
it's also pretty well known that seafood is generally better in colder weather, so sashimi in hokkaido is supposed to be the shitz. especially with uni.
but in tokyo, along with daiwa in tsukiji like others have mentioned here, you generally get better sushi in downtown (like kanda and ueno) as opposed to other areas. i guess that's where sushi in tokyo started.
I've had fish in hokkaido, while ridiculously cheap and good, I feel like their best catch gets sent to restaurants in Tokyo. Then again I was eating shitloads of uni not in season.
just pmed you some links