The majority of travel done within the city is by train and subway. Japan has one of the fastest and most efficient transport systems in the world but it can be a bit daunting at first.
Some helpful links to help plan your journey
Jorudan Train Route Finder
Our Out & About section also has links to barrier free stations and a site to help you see which stations are stroller friendly.
Tokyo Stroller also has a comprehensive resource section listing some other great sites for helping you find your way around Tokyo. Their list includes links to English speaking taxi services and how to use the airport bus as well.