The best museums are in
The winner is Mexico City
Cosmopolitan yet ethnic and with lovely colonial sections, Mexico's huge, smoggy capital offers great food, great (well-dressed) people, and tons of sightseeing, galleries, and museums. It's well situated in the heart of the country, with lots of international flights.
Mexico's best archaeology museum, an amazing museum at the ruins of Tenochtitlan, at the Zocalo, plus dozens of other museums1
And the runners up are....
Many museums of art, culture, and its fine ceramics tradition
The archaeological museum is one of the finest in the country.
Puebla has the country's largest number of museums after Mexico City
Diego Rivera Museum, Quijote Museum, Mummy Museum, and others
Tour ruined San Juan de Ulua Fort; city museum & maritime museum
Several great museums including a mask museum .
Fine art and several small regional history museums
Lovely cultural museum housed in monks' cells, at Santo Domingo monastery. Good museums of contemporary art (MACO), and archaeological finds at Museo Rufino Tamayo
Southern Yucatan State, Yucatan
The new Cacao Museum on the Ruta Puuc is well worth a visit; Uxmal has a museum, too.
Small museums in pirate-proof bastions of yore