While they may be a tad more expensive than the average Tokyo craft-beer bar, this small chain (with branches in Shinjuku, Akihabara and Tokyo Skytree) does its own importing, and carries some interesting beers that you won't find elsewhere in town. Their food menu is also a bit different from the usual sausage platters, with various dumplings, noodle dishes and special beer-friendly starters like Chinese chicken tartar with sesame cream sauce.
Budget around Y4000 for food and drink at dinnertime. They're open all through the afternoon on Saturdays and Sundays.
This book will introduce you to more than twenty of Japan's favorite specialty foods that are less well known abroad, along with a guide to the best places in Tokyo to try them and expert tips on what to order. From Bento.com.