It's certainly unexpected, but perhaps the best craft beer retailer in Yokohama is this bayside branch of 7-Eleven. Located in front of the Yokohama Hammerhead shopping complex and ship terminal, they attract craft-beer fans from around Japan. They currently stock more than 500 canned and bottled craft beers, both domestic and imported, and are reportedly aiming to reach 1,000.
Note that not all the beers are found in the same place - don't miss the fridges full of Japanese craft beers near the back of the store and the aisle of Belgian beers nearby. There's also a good assortment of beer-friendly snacks, perfect for when you want to enjoy an outdoor beer on one of the benches looking out over Tokyo Bay.
You can even shop for glassware appropriate to different styles of beers. And of course they're open 24 hours, so if you need to restock your craft-beer supply in the middle of the night, this is the place to do it!