I was surprised at how easy it was to visit my first manga cafe. Gera Gera is l ocated right on Roppongi Dori, although the entrance is a little small and you have to climb to the 6th floor. As soon as I walked in, the attendant friendly attendant explained the procedure to me in English, and ushered me to an English computer. There are about 40 tiny booths, equipped with a computer, web cam, and headphones. You can print anything you over the store's printing network. There are vending machines, cup ramen, magazines, snacks, and shelves of manga - everything you need to chill for an afternoon. I noticed several Americans using the computers to check email etc.
There are useful computer directions printed in English.
Gera Gera doesn't have any private rooms, but it was very quiet and other people were not a problem. I paid 400 yen for my first hour.
I'd definitely go back if I was in the city and needed to surf the net or watch a movie. I can't read the Japanese manga, but there's plenty of it if that's your thing.