We went to the ruins in Costa Maya and really enjoyed it. Did an 8 hour tour. Most of them you could climb on...even a big pyramid. It was a very nice tour done through the ship. I recommend the ship's tour in case you run late...they will wait for you.
I have visited Mayan ruins in Belize, from the port of Costa Maya and been to the ruins at Tulum. I have also visited Chichen-Itza from the port of Progresso / Merida.
I can tell you hands down that of all the above mentioned, Chichen- Itza is by far the largest and most beautiful.