At one time or another I think that I've gone with all of the tour operators that have a tribal permit for Upper Antelope. I really like the guys at Overland Canyon Tours, check'em out and don't forget to make reservations well in advance:
A few things to keep in mind are (in no rational order):
Don't freak-out over the crowds at Upper Antelope. I've seen pro-level photographers (who were not "emotionally prepared" for the throngs) curse their guide to the bone, throw gear in frustration, & storm out of the canyon.
Most all of the tour guides work together incredibly well. The "regular tour" guides do a great job of keeping their tourists moving quickly past the tripods on the "Photo tours." So well in fact that a 30-second exposure (standard stuff in the slots) will generally do a good job of making all the people disappear.
If you are still frustrated by John-Q-Public getting in your shot, just tilt your camera up a bit. Without the canyon floor in the shot, there will generally not be any obvious horizon or "proper" orientation, so just go ahead & tilt your camera in any way necessary to get Little Timmy out of the shot.
Remember, your basically taking pictures in a cave. Your eyes have adjusted, so you can see just fine, but it really is pretty dark. So under-expose accordingly. That's how you get the deeply saturated dramatic photos you see everywhere.
Don't forget Lower Antelope Canyon! It's smaller, tighter, and you don't have the "light-beams" of its big brother (the more famous Upper Antelope), but it's less crowded and more relaxed. Also, at Lower Antelope if you can convince the caretakers that your gear is "Professional" enough, you can be allowed to enter on your on without having to be part of a guided tour. And before you ask, I have no idea how they judge gear to be professional-enough. I'm generally dragging-ass with more than $20K of gear, while my wife is happily bouncing around with a 5-year-old Rebel, and we both have always been waived in without any problem.
Finally don't go just once and think that you've seen it all. The light in the morning, mid-day, and afternoon is dramatically different. Pictures of the exact same sandstone formation will look completely different taken at different times of the day.
Thanks so much for taking the time to write such a detailed response. Really appreciate it. Hope it'll be a fruitful trip.