Hard to decide for me. Both are gorgeous. I think 3D version looks more refined, whereas anime version makes her look more unique and anime like to me. From an anime game perspective, I don't think the 3D version of her face looks as good as her anime counterpart, so if you want to make it an anime type horror game, you should probably stick with the anime version but make it a little bit more refined like the 3D version.
If you decide to go with the anime version, I suggest this: add shadows (or at least her shadow) like in the 3D version, make her nose and mouth look a little more visible as they can barely be seen in this picture (maybe they are actually more visible in game?). If the lamps in the anime version are turned off, make them look turned off like in the 3D version.
TL;DR: I vote anime version (with some refinements if possible). I will probably still like the game regardless of which version you go with.