How safe are airplane tours of the Grand Canyon?
It used to be worse. (Comforting, I know)

Back in the day (1956), commercial airliners traveling coast to coast would often give their passengers a little tour of the Grand Canyon on the way to their destination (air travel was still a novelty).  When a mid-air collision between two passenger planes occurred, the government invested in a $250 million upgrade (1960 dollars!) of the air traffic control (ATC) system. One could say that the crash resulted in the 1958 creation of the Federal Aviation Agency (now Administration) to oversee air safety.

One of the things the FAA did was create a Special Flight Rules Area (SFRA) around the Grand Canyon and make a specific chart just for the area. Additionally, they created approved commercial tour routes (see the orange routes below)



In addition to commercial sight-seeing tours being more regulated, there is a lot more training, documentation and procedures available for pilots with the main interest being safety. For example, the following notice is printed on the chart (References 14 CFR Part 93 Subpart U which gives minimum altitude restrictions, both for safety and noise abatement!)


https://skyvector.com/?ll=35.7929449938479,-112.79126822365794&amp;chart=231&amp;zoom=2

And of course, as mentioned in another answer, commercial operators, even if they are operating what looks like a "small private plane" are subject to increased mechanical inspections and regulations. One thing to look for when you arrive is the level of professionalism exhibited by the crew (it might just be a single pilot), but also the people checking you in and working with you to get you on your flight. There is something called a "culture of safety" in aviation that, while the unforeseen can always happen, if there is a culture of safety, preventable incidents can be minimized or eliminated.