These are books I can pull up at the moment. If you have any more particular interests (culture, politics, religion, historical linguistics, historiography, other Andean cultures), I can help you with books, articles, and other resources that focus more on those.

General Coverage

D’Altroy, Terence N. 2003. The Incas. Malden, Mass.: Wiley-Blackwell.

Shimada, Izumi. 2015. The Inka Empire: A Multidisciplinary Approach. University of Texas Press.

D'Altroy's book is frequently used in intro college courses, for good reason. It's not the most up-to-date, but it covers a large amount of material and is cheap. Shimada's is not cheap, but better, very nicely illustrated, and most chapters can be found in PDF form somewhere online.

Inca Religion

Bauer, Brian S., and Charles Stanish. 2001. Ritual and Pilgrimage in the Ancient Andes: The Islands of the Sun and the Moon. University of Texas Press.

Gose, Peter. 2008. Invaders as Ancestors: On the Intercultural Making and Unmaking of Spanish Colonialism in the Andes. Toronto; Buffalo: University of Toronto Press.

Meddens, Frank, Colin McEwan, Katie Willis, and Nicholas Branch, eds. 2014. Inca Sacred Space: Landscape, Site and Symbol in the Andes. London: Archetype Books.

Valera, Blas, and Sabine Hyland. 2011. Gods of the Andes: An Early Jesuit Account of Inca Religion and Andean Christianity. Penn State Press.

These books combine archaeological research with colonial era accounts to describe Inca religious practices, both before and immediately after the Spanish conquest. The Bauer and Meddens books are more archaeological, Gose is mostly ethnohistory, and the Valera and Hyland is the first English translation of a rather unique colonial-era document with insightful commentary.

Contact Period

Burns, Kathryn. 1999. Colonial Habits: Convents and the Spiritual Economy of Cuzco, Peru. Duke University Press.

Lamana, Gonzalo. 2008. Domination without Dominance: Inca-Spanish Encounters in Early Colonial Peru. Durham: Duke University Press Books.

Mumford, Jeremy Ravi. 2012. Vertical Empire: The General Resettlement of Indians in the Colonial Andes. Durham, NC: Duke University Press.

These three books together provide a good account of the Spanish conquest. Lamana covers the initial period and the years immediately following, portraying a Spanish occupation constantly at odds with itself, a Quechua nobility manipulating the situation to maintain its power, and a lower class overrun by yet another imperial power. Mumford examines the period after Spanish control stabilized (to some extent), and Burns takes a close look at one particular interface of the Spanish empire and local residents. Each is solidly in the field of history.

History

Garrett, David T. 2005. Shadows of Empire: The Indian Nobility of Cusco, 1750-1825. Cambridge University Press.

Silverblatt, Irene Marsha. 1987. Moon, Sun, and Witches: Gender Ideologies and Class in Inca and Colonial Peru. Princeton University Press.

Thomson, Sinclair. 2002. We Alone Will Rule: Native Andean Politics in the Age of Insurgency. Univ of Wisconsin Press.

These books touch on the persistence of indigenous culture through the later colonial years.

Ethnography

Allen, Catherine J. 2002. The Hold Life Has: Coca and Cultural Identity in an Andean Community. 2nd ed. Washington, D.C.: Smithsonian Institution Press.

Allen, Catherine J. 2011. Foxboy: Intimacy and Aesthetics in Andean Stories. Illustrated edition. Austin: University of Texas Press.

Skar, Sarah Lund. 1994. Lives Together--Worlds Apart: Quechua Colonization in Jungle and City. Oslo, Norway; New York: Scandinavian University Press; Published in the United States by Oxford University Press Inc.

Weismantel, Mary. 2001. Cholas and Pishtacos: Stories of Race and Sex in the Andes. University of Chicago Press.

These are essential ethnographies by cultural anthropologists. Foxboy gets a little weird and conceptual at times but is all the better for it; just don't start with that that one.

Kind of Fiction?

Allen, Catherine J., and Nathan Garner. 1996. Condor Qatay : Anthropology in Performance. Prospect Heights, Ill: Waveland Pr Inc.

Isbell, Billie Jean. 2009. Finding Cholita. 1st edition. Urbana: University of Illinois Press.

Condor Qatay is a stage play and Finding Cholita is fictionalized memoir; both are based on their author's personal experience and research in Quechua communities. They are also both wonderful, accessible ways to be introduced to 20th-century Quechua culture.