Leave the Inn after breakfast, head north on Rt. 89 and take the turn toward Sunset Crater. This is an extinct volcano and lava flow with a visitor's center and a nature trail. Continue on this road to Wupatki. Here is a well-restored pueblo style ruin.
Signs point out a couple other ruins off the main road.
I like the Citadel. Continue on this road to rejoin Rt. 89 and turn south back toward Flagstaff. When you get back into town, catch eastbound Interstate Rt. 40 at the first opportunity.