A friend and I had a Navajo taco for breakfast at El Tovar five years ago and she's still talking about it. Sane eaters would probably split one of these (spiced but not spicy) behemoths, but we each got our own. I don't actually remember what's in it, but it's basically egg-sauce-meat filled Indian frybread and I remember smiling after every bite.
If you are going to the South Rim - you basically have 2 options..
inside the park and just outside the park in Tusayan.
Inside the park:
Dining room at El Tovar. There are dining rooms at Bright Angel Lodge, Yavapai Canyon Cafe and the like. http://www.tripadvisor.com/Restaurant...
I ate at a steakhouse in Tusayan a few months ago..nothing memorable.
So I can't say that there is anything there that is fantastic.
Although if you are at the North Rim - the cookies at the Jacob Lake cafe are to die for..some of the best cookies I've ever had.