Indonesia is geographically and biologically complex. Composed of over 17,000 islands, it is home to 15-16% of the world’s bird species. Field guide coverage is spotty; which guide(s) you will need depends on which islands you are birding.
West Papua (formerly Irian Jaya)
Western New Guinea; Numfor, Supiori, Biak, and Yapen islands and associated islands in Cenderawasih (Geelvink) Bay; Waigeo, Batanta, Salawati, Misool, and nearby small islands off the western tip of New Guinea; Aru Islands.
Birds of New Guinea (ISBN 978-0-691-02394-6) by Bruce M. Beehler, Thane K. Pratt, and Dale A. Zimmerman covers the region fairly well; really, it is your only choice. Unfortunately, the guide was published in 1986 and is out of print. Copies occasionally show up online for exorbitant prices (hundreds of dollars). For more information about the guide, see the Papua New Guinea page.
A new version of the guide is due out sometime soon. In 2006, it was rumored that the guide would be released in 2007. As of December 2007, some references are citing April or May 2008, while Half.com is saying 2009. In March 2007, I asked Dr. Beehler about the forthcoming guide, but he would not (could not?) give me an answer. I hope whatever difficulties or delays have occurred will be resolved soon!