When I fish the gray reef area, we usually stay at the Sunset bar & grill on Hwy 220 (307)472-3200. Their rates seem reasonable and the rooms are nice and clean. I'm sure the lodges in the area are also nice.
You can also camp along the river in a few spots, or down on BLM land below government bridge. If you are going to fish on the GR section, beware that you can only keep one fish over 20"/day, and I've been checked by Fish&Game 3 times up there (I never keep any trout from this area, but many people do, which is one reason the fishing has really gone down hill over the last 7 years).
Here is a helpful BLM map of the area http://www.blm.gov/pgdata/etc/medial...latteGuide.pdf