If you are going to compliment a woman you don't know all that well on a body part, eyes is generally a good way to go. That being said, complimenting a woman acting in a professional capacity on her appearance is generally in bad form. It's something that has often been used to undermine a woman and to remind her that she's really just a sex object who doesn't belong in the "world of men." Clearly, that wouldn't be YOUR intention, but there's such a long history of it that I would never recommend doing it.

Women are so over-sexualized all of the time, that a non-physical compliment does show a lot more thought and appreciation of her as an entire person.