Navitime is one of the main navigation services in Japan.
The interface is very easy, with a small icon as your virtual self walking along your route on your phone's screen.
Apart from Navitime, there are other companies offering navigation services.
One alternative I quite like, and cheaper than the paid version of Navitime, is the paid version of ‘Norikae Annai’ by Jorudan (2,99$).
Both apps are also available in Japanese.