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Not sure exactly what your qualifications are but... I like Blue Bottle Coffee -- It has several locations in Tokyo and really good coffee!
You can certainly check out Fuglen at Shibuya in Tokyo - very good coffee, Norwegian vibe. Omotesando/Harajuku area is certainly brimming with cafes as well. Streamers Coffee Company, for example. And also, Toranomon Koffee!
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