I love them both, and they're staged so differently (Nemo is on a big, traditional stage, while the Lion King is theater-in-the-round, with sets on floats that are paraded in from the corners) and tell such different stories, with such different styles, that it's a bit of an apples-to-oranges comparison to try and pick a favorite.
That being said, I personally prefer FOTLK, simply because I find its music and theme to be more engaging to me personally. If you have time, though, I'd try to squeeze in both. For me, those two shows are easily the best live shows anywhere on Disney property.