If you're having trouble finding craft beer in Tokyo, this site is your friend:
http://tokyobeerdrinker.blogspot.hk/
Pretty much any good liquor store in Tokyo will have some craft beer. You can get Yo-Ho at most Lawsons convenience stores, too – these are pretty solid, especially the Aooni IPA, Tokyo Black porter and whatever is in the their "Sorry" series of one-offs.
If you're in Shinjuku, check out Shinanoya for a decent beer selection. There's a liquor store inside Bic Camera that is also decent. On the east side of town, Le Collier inside Tokyo Station has a great selection of good Japanese craft.
For draught beer you're spoiled for choice... Popeye's is incredible, they have 70+ extremely well-curated taps. The Baird taprooms are good too, Craft Beer Market has a decent selection and is very cheap for Japan, Goodbeer Faucets is nice and I like the Watering Hole. One of my favourites is Kura Kura, an obscure upstairs place with 12 interesting beers on tap. There are actually tons of little neighbourhood craft beer bars with just a few taps that rotate quite often.
Some good Japanese breweries to check out:
- Hitachino Nest (good lager and witbier)
- Yo-Ho (mentioned above)
- Shiga Kougen (try the special IPA, it's great)
- Fujisakura Heights (great rauchbier)
- North Coast (excellent hoppy West Coast-style IPA)
Definitely hit up Popeye's, though. You won't regret it. One of the best beer bars in the world.