Born in Blood & Fire: A Concise History of Latin America by John Charles Chasteen might be something to look at.

Great book on the history of South America (plus the Caribbean too). It does include more than just the time period you asked for though, starting with the encounter between the Old and the New Worlds, going through colonialism, independence, and ending with the Cold War. So, if you are looking at a deep dive just into colonialism, I would not recommend this book. But if you are looking at the broader themes of what colonialism in South America looked like and how it has helped evolve the history of South America, then I would definitely recommend.

My go-to recommendations:

• Vertical Empire: The General Resettlement of Indians in the Colonial Andes by Jeremy Mumford looks at how Spanish economic and political systems destroyed, borrowed from, or integrated themselves into existing Inca institutions. A great introduction to the the early colonial period.

• Invaders as Ancestors by Peter Gose is far and above my favorite book on the colonial period. It's dense, but not too "technical" for an average reader. Gose tackles the complexities of Spanish Catholicism in the Andes and the indigenous response to it.

• From Silver to Coacaine, ed. Steven Topik, Carlos Marichal, Zephyr Frank, does not exclusively cover South America, but many chapters do. It looks at the beginnings and modern continuation of exploitative commodity industries in Latin America.

• Modern Inquisitions by Irene Silverblatt makes the argument that the Spanish Inquisition, as realized in South America, represents the beginnings of "modern" institutions. Her other book, Sun, Moon, and Witches: Gender Ideologies and Class in Inca and Colonial Peru covers much of the topics without the take-home-message.

• Negotiated settlements : Andean communities and landscapes under Inka and Spanish colonialism by Steve Wernke is tidy case study of historical archaeology and how Spanish rulers and local elites established control through geography.

• Death and Conversion in the Andes: Lima and Cuzco, 1532-1670 by Gabriela Ramos, as the titles suggests, covers the indigenous fight to maintain traditional burial patterns, which formed a large part of religious and ethnic identity.

Malintzin's Choice by Townsend is a great resource on the period of Cortez in Mexico. It focuses on a very controversial individual in Mexican history. A great insight.

Also I feel obliged to mention your local library as a great resource, don't be afraid to hunt down a librarian and ask them for book advise.