ANIME RELATED PUBLISHING
The main companies in the publishing industry are the "Otowa group" of Kodansha (publishing the Shonen Magazine line) and Kobunsha and the "Hitotsubashi group" of Shueisha (publishing Shonen Jump line of manga magazines), Shogakukan (publishing Shonen Sunday manga magazine) and Hakusensha (publishing Young Animal manga magazine). King Records, which is now independent of Kodansha's record division, is also sometimes included in the Otowa group. I think the names Otowa and Hitotsubashi refer to the fact that the main offices of the various companies are located in the Otowa and Hitotsubashi areas in Tokyo. Anyway, the two groups have been rivals for a long time.
The third main group in anime related publishing is the Kadokawa Holdings group. Within that group, Kadokawa Shoten publishes Newtype magazine and Media Works publishes Dengeki line of magazines including Animaga. Kadokawa Holdings has also absorbed Enterbrain, which publishes the game magazine Famitsu.
Then there are the independent publishers (independent in the sense that they tend to have a more independent role in the world of anime, rather than that at large) which include:
Source: Animation Grand Prix magazine (published by Shufunotomo Infos Jouhou Sha).