If you're craving great pizza on your travels, I have to recommend Devilcraft to you - which has three locations now in the Tokyo Metropolitan area (in Kanda, Hamamatsucho and Gotanda).
The deep dish pizza that we had when we visited was called "The Devil Works" which has pepperoni, salami, sausage, mushroom, red onion, green pepper, spinach, fresh tomato, black olives and stuffed green olives. It was just the right mix of flavors and it was cooked perfectly. Be warned though, they do advise in peak times it can take up to an hour for them to prepare and cook your deep dish pizza - so if you're in a hurry it might not be the best idea! They do also have a minimum of one drink per customer policy, so bear that in mind too.
Devilcraft will appeal to you even more if you're into craft beers - they have multiple types available on tap daily. They list what is available for the day on their website, so if there is something in particular you like you can always check ahead of time to see what's available.
The Kanda location where we visited is relatively small, so we called and made a reservation for the night we visited. I would recommend doing that if you are wanting to avoid waiting around for a table to free up - it is a popular spot and they do get quite busy! They have English speaking staff there too, so even if you don't speak Japanese it shouldn't be difficult at all to make a reservation.
The Devilcraft website can be found here and it contains information about all three store locations, the menus, opening hours and access information on how to get there.
I hope if you try it you enjoy it as much as we did!