If you are just in Somoto to see the canyon, consider staying with one of the local families in the village of Sonis (right by the reserve entrance) as part of their community-based tourism project. Homestay accommodations are in purpose-built cabañas right next to family homes. Sleeping right next to the canyon will give you plenty of time to get out and explore as well as the chance to experience life in a rural community. You can eat excellent, inexpensive meals with your hosts.
Alternatively, there are some nearby lodgings with availability below.