The ruins in Cozumel may be too long of a trip for your boys. The trip in Costa Maya is shorter. I haven't done either of these but plan to go to Chacchoben (Costa Maya) in April. It is a five hour trip. I think the ruins in Cozumel are about a 7-8 hour trip involving a long bus ride.
There are multiple ruin sites in Costa Maya. The biggest ones (Dzibanche & Kohunlich) are a two hour drive each way. Chacchoben is only a 45 minute drive but smaller ruins. A Gentleman named Ivan grew up at the Chacchoben ruins as a small boy, he offers independent tours to any of the mayan sites out of Costa Maya. He has a web site www.chacchobenruins.com. The Mayan ruin sites out of Cozumel are smaller than any at Costa Maya. It is about an hour drive to the ruins but also about 20-30 minute ferry from Cozumel to Playa del Carmen.
I would recommend the Chocchoben ruins in Costa Maya then some beach time in Cozumel. Cozumel has a lot of beachs to meet different needs. Have Fun. Lonnie