I've gone to both Upper and Lower a couple of times, and had somewhat different experiences each time.
I used Carol Bigthumb's group (it appears it's now called Adventerous Antelope Tours, as mentioned by a couple of people above; not sure it had that name when I went) for Upper both times, had great experiences with their guides. Bit of Trivia, Carol's grandmother was the person credited with discovering Antelope canyon while shepherding sheep.
Her son Lionel is one of the guides, and is an avid photographer. He'll sometimes take photogs to other nearby locations off the official list on their website, although I haven't employed him to do that (yet).
Nov 2011 - Very few people out there, which was great. For Lower Antelope, I did the photography tour. The Navajo website says it's a strict 2 hour limit, but they said if I stayed longer, I could just pay $20/hour extra. I stayed about 3 hours and paid the extra $20 on the way out; would have stayed longer, but I had to hit the road. Not sure if things were just lax because it was pretty deserted or if the policy wasn't re-enforced much back then. Oh, and didn't get any sunbeams inside the canyon, not the best time of year (angle of the sun).
May 2012 - Prime 'sunbeam' time, so Upper was a madhouse. The tour guides did an admirable job helping keep other clueless and selfish tourists away so we could get our shots. Lower was a bit crowded, which made shooting a bit difficult. Just after 2 hours we were kicked out; when I related my earlier experience and offered to pay an extra $20 per person (I was leading a couple of friends through), they said they had to crack down due to some difficult photogs in December. Also, once out, we weren't allowed back in, it was strictly one visit per day. I plan on going back someday, hopefully that's not still a limitation when I do.
If you have two bodies, consider bringing them both with different lenses; you don't want to have to switch lenses in there! It can seem still and fine, then suddenly there's a gust of wind and fine grit flying everywhere.
NOTE - There was a flash flood there recently; I'd call and check for the current conditions before your trip. And if they say there could be rain in the area when you visit, you probably can't get in. It can be sunny and clear at Antelope but rain miles away can flood the canyon. People have died in there that way.