Go to Harajuku! Also available at many food courts
When you say crepe in Japan, it's basically a type of sweets or desserts. Crepe itself is not much different from ones in other countries, but its fillings are whip cream, ice cream, chocolate, fruit... so sweet and wild.
They are originally from Harajuku, Tokyo, and you can easily find them in Takeshita-dori there. If you are not lucky enough to be in the area, you can still enjoy them in many of the local food courts - they typically have one outlet that carry crepes.