It really depends on what you would like to pay. Drury is nice, but they are pricey. I personally like InnSuites. The rooms are clean, and you can find decent rates online or call and negotiate. Howard Johnson's is pretty decent as well. Best Western, depending on which one, is good, as well. So are most of the properties on Woodland Villiage Parkway, by Wal-Mart when you come into town. Though, I can say, for some odd reason, there are quite a few car break-ins at both Motel 6 hotels. I have seen it in the Police Report in the newspaper frequently enough to stick in my mind.
I have stayed in some of the smaller motels up here, pretty much on the west side of Flagstaff on Rte. 66, and they are decent, too. It just really depends - are you going to hang out in your room all day and take advantage of the jacuzzi tub, fireplace and all of the amenities, or are you going to ski all day, party until midnight, and then sack-out and start again? Knight's Inn across from Drury isn't AMAZING, but it's inexpensive, the rooms are basic (and actually a little bigger than Drury Inn's rooms), and they are cometitively priced.