I've been to Bali twice in November/ December (08/09) and found it excellent diving. From the dive sites i've been to - Padang Bai, Tulamben, Kubu, Secret Bay (Macro!), Menjangan and around Nusa Penida I think I enjoyed Nusa Penida most. Guaranteed Mantas at 'Manta Point' (sic!), pelagic sealife in abundance all around the island. Did a lot of amazing drift dives there, although the current can get tough at some spots, e.g. Blue Corner or Crystal Bay.
When it comes to dive shops in Bali I'd recommend BlueBubble Bali, since Christian arranges individual trips exactly according to your expectations. Located in Padang Bai he covers the whole island including Nusa Penida.
However, what turned out to be the most stunning overall package was staying at the island Nusa Lembongan and diving Nusa Penida - drastically shortening travel time to the dive sites and inceasing the overall experience: Most beautiful beaches I've seen in Bali (you'll need a scooter though) and a much more laid back atmosphere compared to other places I stayed at. There are about five dive shops located at Nusa Lembongan, I had chosen a pretty basic one (located at the far end of the beach towards the light house, next to the decent Linda Bungalows) - great value since we were only two divers + guide all the time. Forgot the name though, guess they don't have a website.
Cheers, max