I went to East Kalimantan (Kalimantan is the Indonesian part of Borneo in the south, with the provinces south, east and west Kalimantan, the two malaysian states are sabah and sarawak in the north, and the country brunei is between sabah and sarawak) in 1995 for a few months travelling around. I felt that this part of the Island had alot of logging, mining etc. and the only Orang Utans I saw were in a refuge. I saw some red monkeys in the trees from a boat, but I also saw lots of animals on chains (also my experience in the amazon).
I think if you want to see animals in the wild, you should go to the national parks. If you choose Indonesia I think probably south or west kalimantan is better than east, but I think that probably sabah and sarawak are the places to go.
I read half of a book called something like ‘On Foot Across Borneo’ that was really interesting. I will have to finish it someday lol. It was due back at the library and I never got it out again.