Since I am from a Christian orthodox country, my church of choice would be the Nikorai-do from Kanda, Tokyo. Officially named the Holy Resurrection Cathedral, Nikorai-do is the main cathedral of the Japanese Orthodox Church.
Located on a hill close to the JR Ochanomizu Station, the cathedral was founded by Ivan Dmitrievich Kasatkin, known a St. Nicholas of Japan (hence the name Nikorai-do). Built in a classical Byzantine style, Nikorai-do was completed in 1891.
Travel Tip: Because the cathedral is opened only at certain hours, if you wish to visit it you should first consult the official church schedule, which can be found on the church's website. As a general rule, it is open on Sundays morning.
And to all of you who celebrate Easter, Happy Easter!
EXIF info:
Nikon D90
Lens: VR 18-55mm F/3.5-5.6G
Focal Length: 22mm
Aperture: F/5.6
Shutter Speed: 1/1600s
ISO Sensitivity: ISO 200