Huaca Pucllana: In the middle of one of Lima's business areas, you'll find a pre-Incan temple made of an adobe and clay between 200 AD and 700 AD. Guided tours will teach you more about the cultures that preceded the Incans. Bonus: the restaurant at the Huaca is one of the best in the city, offering dinner views of the lit-up structure.
Museo Larco: Inside a mansion in Pueblo Libre, you'll find one of the largest collection of huacos, pre-Incan and Incan ceramics, including a room full of erotic depictions. The Larco Museum is one of the only ones that lets you into their storage room so you can see what's not on display.
Museo de la Nación: Though this museum has seen better days, the key exhibit here is Yuyanapaq. Created by the Truth and Reconciliation Committee in the early 2000s, it displays photos, videos, and audio recounting terrorism in Peru during the 1980s and 1990s.