I've been to the area twice, most recently this past June. First trip we stayed in Playa del Carmen and took a day dive trip to Cozumel. This year we spent most of our trip on Isla Mujeres but added a few days in Playa just to dive the cenotes.
Playa: We used the same shop both times in Playa and I highly recommend Gerardo and Irene at Scuba10 for ocean or cenotes diving. Cenotes may not be for everyone, but you have to try at least once imho. Work with the shop you choose to select a cenote based on your comfort level with buoyancy/visibility and what you'd like to see (halocline, stalagtite formations, jungle, cavern openings to pop up into, etc). I think it is Dos Ojos that has a mid-dive surface into the jungle.
You can do a cenote and Tulum or Coba in a day, but you need to plan carefully. Many cenotes are a healthy drive down an unpaved road into the jungle. One of our favorite cenotes is El Pit and it is around 40 minutes off the highway down dirt track. Most are closer.
Whalesharks: We did two days. My wife did a day out of Cancun, I believe with "whale shark daddy". She was very pleased with the boat and service. The next day, we went together from Isla Mujeres with Mundaca divers. We booked both just a day or two ahead. Granted, Isla did not seem to have many tourists at the beginning of June. But it seems that at least a few of the shops work together to organize people onto boats for any given day. I wasn't very impressed with Mundaca divers' boat or service, but they got the job done. I think the Cancun shop was ~$125 and from Isla was ~$105 including wetsuit. Both days were amazing in terms of interaction with the whale sharks. The experience here was different from our previous encounters in Maldives, Galapagos and La Paz. Everywhere else, we swam hard to keep up with the one or two sharks that would appear at a time. Here, we just sat in one place and let them come to us. At times, we had 3-5 mouths to dodge. Photography was frantic.
Pyramids: Tulum is closest to Playa del Carmen and can be reached by public bus ~1hr if I recall. Coba is a little further, but I don't know if there's a direct bus. Chitzen Itza is a couple hours and there are many tours that will take you. We've done Tulum by bus and rented a car to do Coba and Chitzen Itza in a day. Tulum is beautifully set on a bluff overlooking the ocean. The ruins are small. Coba is set deep in the jungle, had fewer tourists and is less redeveloped. Chitzen Itza is large with amazing ruins, but heavily touristed and a good hike from Playa. Depends what you enjoy. But Tulum is so close it is sort of a no-brainer for a half day.
Playa- we like this town. It is compact and there is good local food within a couple blocks of the tourist strip.
Hope that helps. Have a good trip.