If you haven't already visited the Mayapan Archaeological site in the Yucatan in Mexico, please do. It was our favorite site by far on our recent trip to the area and would definitely recommend a visit to this spot. You'll likely have the place all to yourselves and can explore with abandon.
The Folk Art Museum - Yucatan in Merida is well worth a visit. It won't take long for you to browse the collection and what they have is an incredible selection of the fine craftsmanship in this area as well as Oaxaca. We found this to be an absolutely delightful way to spend an hour or so while in Merida.