Best time to dive sipadan and its surrounding area is between April - Nov. Most of the accommodation service providers will operate their own dive centre. Diving at mabul, kapalai and si amil island can be arranged thru walk in basis.
Do bare in mind that in order to dive sipadan, you will have to book with the dive operator in advance (3 months) as the government only issue 120 of them daily. The more reputable big resorts will have better quotas. Generally speaking most of the good resorts are located at the east side of mabul. (Smart, SWV, Scubajunkie, Borneo Dive) Seaventure was an oil rig and now is transformed into a dive resort. The rest of the homestay style accommodations are along the western coast of the island.
You may also stay at Semporna (Sipadan jetty town) where you will have access to the northern islands such as Bohey Dulang and Gaya.
Summary : Best months April - Nov. Loads of accommodations to choose from. Book your Sipadan Dive as early as possible.