George, the wet season is usually in Dec. So crossing to Penida/Lembongan can be a bitch. So if she is into macro, have her stay at Scuba Seraya and dive the area (including Seraya Secrets, the wreck and the surrounds). If viz goes to crap, and it can when it rains due to run off, go to Menjangan up north and Secret Bay, which is also a great muck dive.
Another area which is pretty decent and not as far is if she stays in Padang Bai and dive the Gili Tepekong and Padang Bai areas. The viz is usually decent there but when it rains, it's not a great place to be.
I've used BIDP for all my diving in Bali since they opened in 2000. Great guides and service. Local owned (ok he's really Javanese but it's the next island) and run. Scuba Seraya has its own dive ops as well but you can also arrange it through BIDP. Have your friend plan a flexible schedule by arranging the diving based on the weather forecast of the next day. It's a pain for the ops but they'll do it. Just don't tell them I suggested it. 
For Thailand, someone already asked the same question in the forum. Do a search in the last few days.
Most liveaboards going out to the SImilans leave from Tap Lamu in Khao Lak. Again there's a plethora of boats so it depends on her budget. Many people made their recommendations in that thai thread.