I imagine competition to work at either of those places is fierce. So isn't the question more, which one is willing to hire you.
If they both are. I... personally... think that's an awesome perdicament to be in. lol. I think I'd go with ILM. But I'm also fascinated with Pixar's computer animation and the types of stories they tell. I know Pixar likes to hire people who are as good with 2D traditional art as they are with 3D because they want well rounded artistic individuals.