Here’s a good little day (or half day) trip from San Cristobal. You can arrange it yourself or do what lazy bones me did and take a tour, because it’s only 250 pesos (about £10) that way anyway and then you don’t need to worry about anything. They drive you down to the landing bay near Chiapa de Cazo and put you on a boat. The boat tour lasts 2 hours. Then they bring you back again.
However you could get the collectivo to Chiapa de Cazo, then a taxi or a long walk to the landing dock and then buy a ticket for the boat there, if you’re really determined to avoid tours at all costs. Not sure how much it would cost that way but not a great saving, just gives you more flexibility about how long you spend there I suppose.