If you have more time than money, I believe its less expensive to do it on your own. Take the water taxi to Belize City (20 bzd one way) and you can pick up a bus right at the Marine Terminal ($20 U.S.) that will take you straight thru to Flores. From Flores you can arrange a tour and transportation from any local company. The total time will probably be 1 day, each way for travel and 1 day for the ruins, total travel time 3 days. Add to the cost 2 nights in a hotel, but you would be spending money on a hotel on Caye Caulker anyway. If you have more money than time, you can do it in a day using Tropic Air or Maya Island Air. I would check out their website for current pricing.