Yes, the northern part of Japan is less densely populated than the south and west, especially Hokkiado. I'm sure there are some wonderful areas up there (never been that way myself).
I know of a couple of decent places around Osaka that aren't too bad, but they still require some travel. There is a nice spot north of Kyoto, I think it's called Arama?, where there is a large temple on the top of a mountain. It's nice and open with only a couple of dim red lanterns that don't interfere with seeing. Only two problems, late in the evening the priests all start their evening services or something, and walk around with their flashlights. It was kind of disturbing, but they completely ignored us as we watched the sky. Second, there seemed to be some sky glow from Kyoto to the south, but I couldn't tell for sure as the seeing wasn't so good that night anyway. I'm thinking of heading back there again in the spring. I'd sure hate to lug a telescope up that mountain path. [img]/phpBB/images/smiles/icon_razz.gif[/img]
An even better place is south of Nara, again up in the mountains but about 2.5 hours from where I live. It's an actual Astronomy-themed resort called "Hoshi no Kuni" (The Land of Stars). It combines a working observatory and planetarium with a hot spring and cabins for camping in. Actually, the combination is a bit too commercial and kiddified for my tastes, but it is conducive for serious observing. You can rent telescopes, which is nice. Unfortunately, I can't tell you what the skies are like there, because the night we reserved (and I took a special day off for) ended up being overcast and foggy. Very foggy. I was very disappointed. We did get to see a halfway decent planetarium show though. I want to go back, but you have to reserve in advance and pay, even if the weather is bad, so I'm not sure I want to risk that kind of money again. It is a nice setup though.
Here's the Hoshi no Kuni homepage. Beware, it's all in Japanese, but you can look at the pictures if you want.
http://www.vill.ootou.nara.jp/hoshi/hoshmain.htm