Today in the Cancun area I'd choose Isla Mujeres. When we were there, we docked in Cancun, but that was a few years ago and less crime at that time. In the Cozumel area, Puerto Aventuras.
Check the travel advisories before going as they're regularly updated.
In spite of the crime in Cancun we've all read about, the Embassy is only putting Quintana Roo at a Level 2-Exercise Increased Caution right now. A lot of violent crime but still no restrictions on US government employee travel. Be very careful, travel only in groups and exercise good judgement as to where and as to your activities. Now is not the time to check out all the Cancun nightlife and head back to a boat in the middle of the night.
We loved Cancun and the Cozumel area but decided against Cancun last year and likely will do the same this year. Too many places I feel safer going to right now. I don't want to be looking over my shoulder or walking around in fear of a gunfight breaking out. Although circumstances may change it, this was our winter to do the Western Caribbean, but if we do, we'll probably do the Caymans, Jamaica and Panama and forego Mexico.