A few options for you...
Wolf Creek Run (www.wolfcreekrun.net) is a RV campground and Fireside Cabins (www.firesidecabins.com) are located right next door. These are located on hwy 160, just east of town, along the San Juan River.
Healing Waters Resort & Spa (www.pshotsprings.com) has both RV hookups and cabins, plus a hot springs pool onsite. Located in downtown Pagosa, backing Reservoir Hill, which offers lots of hiking and mountain biking options from your door.
Elk Meadows Resort (www.elkmeadowsresort.com) is about 4 miles east of town on Hwy 160 (towards Wolf Creek Pass)- they have cabins and RV hookups. Also located along the river, although river access is a little more challenging.
Sportsman's Campground and Mountain Cabins (www.sportsmanscampground.com) is another option - located on Piedra Road in the national forest. This one is the least accessible to town, but is an amazing area. Located near Williams Creek Reservoir and more trails than could be explored in one visit.
Good luck and let me know if you have any other questions.