MissDoo, have you considered staying in Tulum instead of PDC or Akumal? I found the reef diving around PDC to be mediocre -- if you want fantastic marine life, skip PDC and spend more time on Cozumel. However, the cenotes around Tulum are incredible and you can easily spend three days checking them out. Can't recommend Nihls at Dream Diving in Tulum enough -- best DM (cave instructor and tech diver extraordinaire) I have ever dove with. Plus, the beach at Tulum is TV commercial stunning, and there are a range of accommodations if you want total R&R after your dives.
If you are committed to staying in PDC, it's probably nicer than staying in Cancun, and you can do the whale shark tour from there. Go see the folks at Scuba Playa -- they are a top-notch shop. They'll arrange the tour for you, leaving around 7:00 am and returning in the afternoon. If you want to stay in PDC, the Hotel la Tortuga is fantastic -- small, boutique hotel, excellent service, comfortable rooms, gorgeous pool and grounds, and not a single kid in sight when I was there. Can't recommend more highly.
One option is to fly to Coz, do five days of reef dives there, ferry over to PDC, maybe spend three days there to do the whale shark tour and a few reef dives, then bus or van to Tulum for four days of cenote diving, then fly out of Cancun. Or do that in reverse.