There's a lot more to Japanese curry than CoCo Ichibanya. I'm not suggesting that you go visit every single run-down Mom-and-Pop curry shop on a wild goose chase for culinary perfection. But if you want to find some higher-quality goods, look for signs that read 欧風カレー: oufuu karee or "European curry."
Is there anything particularly European about it -- more so than regular Japanese curry, I mean, which entered the country through English cuisine? Not that I can see. My experiences with "European curry" have simply been that the ingredients are top-quality and the flavors much more robust. You'll pay a little more -- more like $15-18 for one person versus less than $10 at a typical curry lunch counter -- but for the serious curry aficionado on a trip to Japan, it's more than worth it.
I covered a small lunch place called Mitsuboshi, which bills itself as "French curry," on Wired.com last month.
I'd also recommend Bondy, with locations all around Tokyo.
Japanese language version: 日本滞在レポート：『ミツボシ』の欧風カレー [Wired Vision]