There are lots of solid beers available in Tokyo (& Yokohama).
I link to some beerworthy English-language World-Wide Web sites on my regular bookmark page.
But I'll break out these two:
1) Boozelist (Chris Chuwy tries to annotate what beers are on tap at scores of beer bars in Tokyo [including the Tama region] and Yokohama.)
2) Japanese Craftbeer events ("Beerkat" [Rei-chan] denotes upcoming beer events, at beer bars, and detached venues.)
Baird has two brewpubs in Tokyo: In Naka-Meguro and in Harajuku; and a third brewpub in central Yokohama.
If you want more venue suggestions, please request them here.
I got to Popeye last night (second night in town). Pretty awesome. Had four 30 cL beers. The Yo-Ho TokyoBlack Porter (hand pump) and Divine Vamp III India Black Ale were both awesome. I only saw one other American there. He said not many Americans go (surprising, it has a very "American beer bar" feel). I thought the prices were quite high compared to Manhattan/Chicago/San Francisco/London but the American guy said they were one of the cheapest places in town.
I noticed one of the places in your first link has Maui Coconut Porter for 1,300 Yen a glass. Probably quite a novelty for people who don't get to the US, but I'll pass (not just on the price, I have no intention of drinking non-Japanese or at least non-Asian beer here).
I'd heard that craft beer was few and far between in Japan. From what I have seen that definitely does not apply to Tokyo. An American client (who lives in Tokyo) said there are tons of places around the office so I will probably have a beer or two with the clients a few nights.
Now I just have to map all of those places based on my understanding of the geography, which is entirely based on the Metro map.