I've been to both, and I can't honestly say that I prefer one over the other because they're so different. I'd love a return visit to each, but at diff. times of the year. We just went to Niagara Falls this summer, and it was awesome! If you go, be sure to stay on the Canadian side. The views are better. Of course, that's also where all the "touristy-schlock stuff" is, as Inigo mentioned. But that's kind of fun in it's own way. I'd love to return to Niagara Falls in the winter when the mist from the falls freezes on everything and it sparkles. They have a winter festival of lights, too, that I'd love to see.
The Grand Canyon is just amazing - you see pictures, but they don't prepare you for seeing it in person. The vastness of it, knowing that it took millions of years to form - truly awe inspiring. It's another one of those places that I'd love to see during diff. times of the year - we were there in July and visited the South Rim only, and I'd love to go back in the spring to see the wild flowers. And I've heard that the North Rim is completely different from the South Rim - there's even one type of squirrel that is ONLY found on the North Rim, nowhere else in the world.