What are the animation studios outside the Tokyo area and why the majority is concentrated in Tokyo?
What animation studios are located outside the Tokyo area?
Japanese Wikipedia's article on アニメ制作会社 (Animation studios) says:
92% of studios are located in Tokyo Metropolis. In particular, most of them cluster around larger studios. Few are found in rural areas.
Looking through the list given further down on the Wikipedia page, we find that the following studios are not located in Tokyo Metropolis (東京都):
Studios included in the "foreign" and "inactive/bankrupt/etc" sections of the Wikipedia article at the time of writing are not included in the above list. Note also that I generated this list semi-programmatically - I guarantee that every entry on the list above is a non-Tokyo studio, but it is possible there are some other non-Tokyo studios I missed. The report cited for the 92% figure on Wikipedia identifies 14 non-Tokyo studios at the time of its writing (2010), so the 18 I have listed above probably cover those studios fairly well.
Why is the majority concentrated in Tokyo?
The report cited in the Wikipedia article does not, unfortunately, speculate as to why there are so many studios in Tokyo. I would imagine that it is mostly a simple matter of Tokyo being the economic center of Japan, but this is mere speculation on my part, and I have no sources to support this.
Aside: the report mentions a trend of studios moving into more-rural areas as a result of advances in technology, making digital animation and data exchange simpler.