Here's the basics to choosing a tour of the Canyon. Essentially, you have two options. Both are fine, just depends on your traveling style.
THE FIRST OPTION is to book a tour from Cusco if this is where you are based. You should pay around $50-$60, possibly a bit more if they include more meals or entrance to the hot springs in Chivay.
Here's the things that may or may not be included - the starred items are what I would consider necessary, and the others are nice bonuses.
*Bus from Cusco to Arequipa and back.
*Transportation to Chivay and back from Arequipa
Ticket to see the Canyon
Ticket to the hot springs in Chivay
One or more meals
*Hostel in Chivay
THE SECOND OPTION is for the traveler on a budget who is willing to be more flexible. Get your own bus ticket to Arequipa and book a Canyon tour when you get there. Tours leave every day and there is nearly always room. If you want to do some trekking in the Canyon, this is also the way to do it. The tours that you can book in Cusco only seem to have the short option, where you look down into the Canyon.
So to sum up: The first option, while a bit more expensive, is very convenient and you have the security of having everything planned for you. But if you are more flexible and want to save some $$, try the second option. Then you'll also have the opportunity to stay longer in the Canyon or in Arequipa if you so desire.