I was there as you posted!
OK, firts thing: due to new regulations, which will ikely change by next year, Galapagos cruises are not allowed to propose diving anymore.
If you want to tour the archipelago and dive, you need to go on a live aboard.
Most of them will not have the licence to do landings, I believe, so in short the cruises can propose either diving, or landing on the islands. Might exist a luxury option to combine both.
The cruise was incredible, the snorkeling during the cruise if well enough.
I guess you have booked already, but my recommendation is to go with guide Juan Manuel Salcedo, with Enchanted Expeditions. I totally endorse this guide.
you can take day trips from Puerto Ayora, on Santa Cruz. 2 dives for 125 to 140 dollars, but they are worth the prize, for what you see in the water. No coral though, be warned.
Recommended and most serious operator: Scuba Iguana
Second comes Sub Aqua, I dived with Rafaello and Lotem, they are serious
These are the only two I would recommend. I dived with another operator, they were cool, but I was a beginner having to take a plane the next day, and the divemaster was oscillating +- 3 meters, getting me lost with my buoyancy, stopping just in time to not follow him to 25 meters on a 15 meters dive... Oh and when I asked a 6 minute safety stop just to be sure, they found it a funny idea...
there are horror stories of divemasters refusing to surface on low air or lost group, or panicking and releasing a diver´s weight belt at 20 meters...
There is a recompression chamber on Santa Cruz, by the way.
The water is bloody cold, and there is a lot of current. But that is what brings the big ones!
They´ll ask you 30 dives to take you to Gordon rocks, where you can see schools of hammerheads. I managed to go with only 18 though, after a first day diving so they could check me out. Saw only one hammerhead, it was a day without current. grrrrr