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Hey Luk,
Whale sharks are actually here year round but in the summer months they are harder to find and there are a lot less around. Early September to early April is the most consistent time with the best visibility in the fall and late spring. I'm sure moon cycles affect the plankton in some way but I've never noticed a difference.
La Paz is definitely worth a dive trip, Cabo Pulmo and Cabo San Lucas are within a day trip and there is enough diving for a 2 week vacation between the three places. Best diving is in Sep/Oct with warm waters and good vis. After aboout November visibility goes down and temperatures drop. Still good diving but the difference between the times of year is quite apparent. Diving in the fall is almost like diving in Asia, in the winter it's definitely west coast diving. Sea lions are the main attraction and diving with the juveniles will put a smile on even the most experienced diver. If you do choose to come in the winter or spring you are able to go whale watching, up close encounters with humpbacks and gray whales are guaranteed.