We dove Menjangen island in April 2013 and stayed in Pemuteran. We used Kokak Divers (a locally run company) and found them to be good and very laid back. We only had one other diver with us and 2 divemasters, so crowding was not a problem. We had to drive with Kokak over to the marina area where they rent boats to go out for the day. The boat was slow, but we were in no hurry having just come from Komodo where we did many dives (and loved them all!). The coral was interesting around Menjangen but there weren't a lot of fish in general. There was also a lot of trash floating in the water in areas. Over our lunch break we hiked a bit on the island and also found lots of litter there. It is a shame as there are some beautiful sites. In Pemuteran we stayed at Tirta Sari bungalows. The place was a great value and had beautiful landscaping. The restaurant on site was just so-so. We used Whidi Kadek as our driver to get up to Pemuteran and to get back down to Ubud--we found his contact information on Tripadvisor. Driving on Bali was crazy and we were glad we hired a driver. The traffic jams near Denpasar will probably prevent us returning anytime soon.
Hope this helps--let me know if you need any more info!
---------- Post added January 3rd, 2014 at 06:21 PM ----------
I might also add that if you can get down to Komodo Nat'l park to dive, do it! A major airport expansion is in the works in Labuan Bajo, and I imagine once that opens they will start receiving more big flights which might make the area more crowded. We stayed at Komodo Island Resort on Sebayur Island and really enjoyed our stay. In the future I would probably skip Bali and go to Komodo and maybe venture around Flores island more. Bali was just a bit touristy for our tastes, although it was a unique place that was worth checking out and the people were lovely. The art around Ubud is also wonderful.