I just got back from three weeks of diving in Indonesia which included East Kalimantan. I really wanted to stay at Sangalaki but got very frustrated by their lack of response. They ignored many of my questions (like updated flight schedule so I could plan my trip) and the only thing they were clear about was where to send my money! I had serious misgivings about wiring funds to this outfit because I thought if they couldn't respond to a customer's e-mails they might well leave me stranded at the airport.
I therefore sent Derawan Dive Lodge the same info. request and got back a very helpful e-mail which answered all my questions within a few hours. I therefore booked with them and was glad I did as it turns out that the resort was in shut down mode and me and my dive buddy would have been the only two guests on Sangalaki for a 3 out of the 5 days we planned to spend on this island, and they were busy noisily renovating some of the thatched bungalows. I spoke to the Sangalaki Guest Relations Manager and told him about my negative experience and he told me lots of guests complain about this and they are still trying to fix this.
Derawan, by contrast, is super efficient and reliable. They have comfortable accomodation (tho. not as pictuersque) than Sangalaki with hot water and air con. It's not luxurious but it's just what you need and clean. The chef is amazing and will cook you what you want. The lunch boxes for the dive trips are the best I have ever had in all the 60 countris of the world I have dived in. The dive center has lots of room to rinse and hang gear and a camera room with multi plugs and voltage. Michael, the young divemaster, has excellent eyesight and is a thouroughly good dive guide. He makes it a personal mission to find the critters you came so far to see and is very friendly. The one downside is they don't tell guests not to molest the mantas and turtles. Green turtles come onto Derawan Island every night to lay eggs--ask the security guard to wake you up to see this incedible sight. Even if its 4 AM, it is worth it. Derawan has some good muck diving--you can see really neat stuff like pygmy sea horse, cuttlefish, turtles, nudibranchs, leafy scorpionfish, stonefish, scorpionfish and mandarin fish right off their jetty. We visited the fabled Wakatobi Resort in Sulawesi after Derawan and preferred the diving in Derawan because it was more varied.
They do day trips to Sangalaki which is a lovely island and you will get to snorkel and dive with the Mantas just off Sangalaki island, but it is a 2 hour trip from Derawan so you will have to pay a surcharge.
Same deal with Kakaban and the jelly fish lake (4 different species). Note that there is a wooden platform erected by Derawan to the lake which is rotting in places so care should be taken in walking here (Derawan has been unable to persuade the folks at Sangalaki and Nabucco to share in the costs of fixing this--according to other divers we met, the latter resorts discourage their guests from going to other islands).
Maratua is also a 2 hour boat ride from Derawan and they only go there if the currents are right for you to dive comfortably and see the big fish action. So if it's important for you to go there, ask them about the tides before booking as we didn't get to go during the week we were at Derawan.
Derawan sees a lot of Italian guests; Nabucco German guests; Sangalaki has Asian dive groups and the odd European diver. You might be able to get a better rate by booking through an Asian dive travel operation.
Oh yeah: you can easily fly into Balikpapan and get a visa on arrival. Don't believe the agents who tell you you will need to pay to fly a customs and immigration guy to check you into the country--get another travel agent. Derawan can purchase ongoing tickets from Balikpapan if you have trouble buying them in your country. (note: you must buy the Balikpapan-Berau flights locally as these aren't sold elsewhere).
One regret I had was that I did not have an extra day in Balikpapan to go and visit the Dayaks, so plan accordingly if you are interested in some topside activity.