TPCi is owned in equal parts by Nintendo, Game Freak and somehow the manufacturers of the card game, Creatures Inc.
So you'd think Nintendo owns 33% of the Pokemon IP through TCPi, except they also have a significant amount of stock (not a majority of shares) in Game Freak. The exact amount isn't known but the result is that Nintendo most likely controls TCPi entirely.
Also, just to head it off - the anime (the other most popular Pokemon product after the video games and card games) is made by Studio OLM (which also did the 1997 Berserk adaptation as well as a truckload of other anime based on Japanese video games) and they have no controlling stake in TCPi whatsoever.