Yahoo Japan is a separate entity from the US juggernaut of ancient times. They run a transportation app called Yahoo!乗換案内 or roughly Yahoo Transfer Information. I live here so I can read enough Japanese to get by. But there is no English version.

There used to be a non-Google English competitor that faded away a few years back. The network is quite dense here in the big cities and disruptions happen. So you'll need something that alerts you to problems along the route. They stopped being tied into whatever API that requires. And it's been so long I forgot what they were called. I prefer the Yahoo one to Google Maps because their algorithm that finds best connections works better in my experience. But that's coupled with me knowing my way around Tokyo okay as well. YMMV.