As for Tokyo outside Ueno market:
I picked up some nice selvedge jeans from Pure Blue Japan (http://www.purebluejapan.jp/about-us/location), they have an awesome deep indigo colour, the thread used to stitch it is also indigo-dyed so you can't really see it.
Also a pair from Kapital (http://kapital.jp/shop/detail/4.html), who do a heavy and rough old-fashioned denim.
Going to Kapital in Osaka. Went to Pure Blue yesterday as well
@Levitz started
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As for Tokyo outside Ueno market:
I picked up some nice selvedge jeans from Pure Blue Japan (http://www.purebluejapan.jp/about-us/location), they have an awesome deep indigo colour, the thread used to stitch it is also indigo-dyed so you can't really see it.
Also a pair from Kapital (http://kapital.jp/shop/detail/4.html), who do a heavy and rough old-fashioned denim.