Population for the California mission areas prior to the Spanish colonization can be found in Sherburne Cook's The Population of the California Indians 1769-1970 (University of California Press, 1976).
A number of recent works have suggested that Cook's figures are too low. These works are too new to be found on the internet, but you might check recent issues of Journal of California and Great Basin Anthropology.
For additional background information you might also want to check:
Sandos, Converting California: Indians and Franciscans in the Missions (Yale University Press, 2004)Jackson, Indian Population Decline: The Missions of Northwestern New Spain, 1687-1840 (University of New Mexico Press, 1994)
Hackel, Children of Coyote, Missionaries of Saint Francis: Indian-Spanish Relations in Colonial California, 1769-1850 (University of North Carolina Press, 2005)
OK...you’re talking about a completely different time period than when Columbus came to the new world...
Cheers!