For general Andean archaeology information, the andean.kulture.org site, maintained by Matt Bandy, is a great resource and source of links to other Andean information on the web. I'd also recommend the series of research pages maintained by various folks at UC Santa Barbara: the Titicaca web server. I have a particular interest in Nico Tripcevich's work on obsidian exchange in the Andes. I'm involved in related work at Stanford; see this description of the Stanford Obsidian Research Team.
One of my Stanford colleagues, John Wolf, is also developing a website dealing with his various archaeological interests.
Some other links to Andeanists who are particularly active on the web:
Bruce Owen
Kevin Vaughn
Elizabeth Klarich
And some generally wonderful, "wow, the WWW is neat", Andean stuff:
Guaman Poma
Harvard's Khipu Database
andes C-14
