Elyastam's answers are all correct. The reason you use the singular verb is because it refers to the ONE thing you like best. If you said, "the things I like best," then you would use "are" instead of "is." And "building" should be plural ("buildings").

should be: What I like best about living in Japan is its beautiful buildings. or What I like best about living in Japan is seeing its beautiful buildings. or What I like best about living in Japan is it has so many beautiful buildings.