St. Peter Canisius Chapel
Chapel at the Atma Jaya Catholic university.
Beth David Synagogue | Jewish Community of Japan
Organizes Jewish services, cultural and social events. Located at 3-8-8 Hiroo, Shibuya-ku.
Community Church
It was built in 1925 by a couple of Americans as a place for their choir for which it is still famous. 
Chabad House of Tokyo
The House is open 24/7 to everyone, Jews and non-Jews. Its aim is to spread acts of goodness and kindness and help people materially and spiritually. Located at 1-25-18 Sanno, Ota-ku.