The Museo de Los Altos de Chiapas (Ex-Convento del Templo de Santo Domingo de Guzmán, Av. 20 de Noviembre near Nicaragua, tel. 967/678-1609, 9 a.m.–6 p.m. daily, US$4) has interesting, if somewhat dated, exhibits on pre-Hispanic cultures, the arrival of the Spanish to San Cristóbal [1], and historic buildings in San Cristóbal. Signage is in Spanish, though there are English-language guidebooks at the entrance.
Upstairs is a temporary exhibit area that often shows impressive art collections. The building itself, the former convent of the Templo de Santo Domingo [2], has been beautifully restored with its high archways, polished wood floors, and thick stone and adobe walls.
Links:
[1] http://www.moon.com/destinations/chiapas/san-cristobal-de-las-casas
[2] http://www.moon.com/destinations/chiapas/san-cristobal-de-las-casas/sights/churches/templo-de-santo-domingo-de-guzman