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For hammerheads your need to go to La Paz, it's about a 2 hour drive from Cabo. There is a seamount there called El Bajo. I've tried a few times but always in the summer, local friends who work in the diving industry told me that the fall (October/November) is supposed to be your best chance.
The whale sharks are in the bay of La Paz from September to April, you are pretty much guaranteed to see them, I have swam with anywhere from 2 -15 in one day. There are a lot of guys on the Malecon (boardwalk) that will take you out for about 400 pesos. You need to have your own gear and there is no guide but it's the cheapest way if you are solo.
I booked a tour for my two kids that included whale sharks and diving with one of the local businesses, Baja Connections. It was pretty good as we swam with them for about 2 hrs and than went on to Balandra where my kids did a discovery dive. I would highly recommend them for any diving you might do in La Paz.