Take a look at this interactive map of Tokyo transportation that displays positions of all the trains in real time. It looks like the website is quite old (2012) and it is in Japanese. So I am not 100% sure everything is quite up to date.
It seems the data are up to date, these databases have been freely accessible for quite some time. It is kind of fun to watch this one :o).
The only problem is that the site is not very useful as-is. I hope they come up with something that is more active, and can tell users about delays, etc.