I think Google maps has come a long way. The maps at Google are mostly Japanese, so it works better if you know the kanji or at least the hiragana for your destination. However, most places we wanted to go we got good instructions from Google, with a couple minor exceptions. Google maps in Japan are run by the Japanese branch so there are some issues with searching in romaji.
Hyperdia is decent if you just use the web interface, and know the names of the stations you need. Unfortunately it can't help you with walking instructions. There's a few places where you need to walk a little bit before you hop the next train.
I am not sure about Tokyo, but I use the standard google maps and explore function (free). It will give me options for car, trains, buses and walking. As an example, I wanted to get from near Kyoto station to Arishiyama last week and it told me how long it would take to walk to platform 32 for the 11:07 train. I also like the gps navigation as it essentially gives walking directions (and a friendly blue arrow) which was useful when in Hakata heading to a hotel that was not on the larger maps - worked perfectly.