I just drove through Sedona this afternoon--pretty busy! If you can't find what you want there, try the village of Oak Creek next, which is adjacent to Sedona. For something different, stay in Jerome, about 1/2 hour up the mountain. It's a funky old mining town, with several old hotels & B&B's. Flagstaff could work, but is about a 45 minute drive. Do the drive via Oak Creek Canyon (Rt 89A, I think), and you get some sight seeing in at the same time. There are also a number of small lodges/cabins along Oak Creek Canyon.
Hilton has branded properties in Sedona, Oak Creek & Flag. I've stayed at the Hilton Garden Inn in Flag and it was ok.
Having just completed a driving tour of our wonderful state with a friend, this is a fairly busy time. Good luck!
JP