Here's some you can look at. I'm planning my trip to Borneo in May 2014 and will be going to a Kinabatangan River lodge for a 2 day stay. I just haven't figured out which lodge to stay at yet. I think I have it narrowed down to Sukau Rainforest Lodge and Abai Jungle Lodge.
http://sitoursborneo.com/borneo/
http://borneoadventure.com/
I plan to put my trip together myself. I'm finding that these tour companies are marking up what they sell 100% I just made a 2 night booking at Mulu NP direct with them. $70 a night for a room in the longhouse. Then I bought RT flights Kuching-Mulu-Kuching from the MH web site for $111 each.