Places I liked on my short (5 day) Tokyo trip. This list is very Shimokitazawa heavy, because I found I enjoyed being there much more so than in the big touristy spots.
Matthew Rothenberg: Angel Stain. Only 20 shots served daily. Worth it if you're a coffee nerd, it's unlike any other espresso you've ever had. Show up at opening at 11am or be disappointed.
Adam McNamara: Unbelievably high quality food. The chicken and 20 vegetable curry with coconut milk soup was perfect. They have an English menu and friendly staff.
Jamie Hutchins: Terminal 1, near gate 34. Make the trip, this place is worth it. In fact go to the airport early. The chef's omakase nigiri set is incredible, but also the wild blue-fin tuna set is insane.