Near Flagstaff, there's Wupatki and Walnut Canyon NM's. Nearby Sunset Crater is an interesting drive combined with Wupatki. Walnut Canyon does require climbing quite a few steps if that is an issue.
Back up in Utah is Hovenweep NM. While there are parts of Hovenweep that extend into CO, the Square Tower complex in UT is especially nice.
Of course there's Chaco Culture and Canyon de Chelly in NM and AZ respectively. Make sure you read the NPS website about roads into Chaco to make sure you go the right way.
Back in CO, I know you said you've been to Mesa Verde, but did you get to Anasazi Heritage Center north of Cortez near McPhee Reservoir? Definitely worth a stop. They can direct you to other, lesser know sites in the area. Ask about the Sand Canyon trail if you can do several miles of hiking.