If you only have time (or patience) for one museum, I recommend visiting the Museo de Metales Preciosos, Calle Jaén 777, where you’ll see interesting gold and silver belts, necklaces, bowls, crowns, and bracelets from both the Inca and Tiwanaku cultures, as well as a Tiwanaku monolith.
The courtyard here is also quite interesting: If you look closely at the ground, you can see the remains of sheep bones, which the Spanish used as home decorations during the colonial era.