Its wise to base yourself on Isla Mujeres so that you are as close to the whale shark aggregation as possible. Literally hundreds of boats show up from Cancun each day so it is important to get to the whale shark grounds early! We go with the first handful of boats that leave the island around 7:30am or as soon as our group has had breakfast. Once we find the sharks, we usually have an hour or two with the big aggregation before the 'armada' starts to arrive from Cancun.
Fortunately, the day boats don't stay very long. By noon or so, the boats start thinning out again and by 1:30 or 2pm our boats are often the last ones still enjoying the sharks. That gives our guests lots of freedom and lots of opportunities to get great images, watch natural behaviours, etc.