Here are two websites I found on the archaeology of Indonesia. They are also added to the resources page, which has a long list of links to other sites relevant to the archaeology of Southeast Asia.
The first site is written in Bahasa Indonesia, which may pose a problem to English-speaking users. The Museum Nasional Indonesia’s website is also a little confusing, but if you explore it deep enough there are guides to the collections in the museums.
Related Books on Indonesian Archaeology:
– Early Kingdoms of the Indonesian Archipelago and the Malay Peninsula by P. M. Munoz
– Southeast Asia: From Prehistory to History by P. S. Bellwood and I. Glover (Eds)
– Ancient History (The Indonesian Heritage Series) by Indonesian Heritage