Since the majority of the hiking and backpacking trails start from the South Rim of the Grand Canyon, this is probably where most people will stay. Xanterra manages several hotels inside the park and Tusayan just outside the park entrance has quite a few lodging options.
If you’re doing a hike off the North Rim of the Grand Canyon or plan on doing a Rim to Rim backpacking trip in Grand Canyon National Park the North Rim lodge is your best bet. There is also the Kaibab lodge outside the park entrance and Jacobs Lake lodge about a half hour down the road.
Havasu Falls isthe most popular hiking option in the western Grand Canyon. Seligman and Peach Spring Arizona are the closest towns and offer several options for hotels close to the trailhead for Havasu Falls.
The East Rim or Marble Canyon has 3 good lodging options for hikers hanging out in this area.