A cab ride to Puerto Juarez will get you to the Ultramar ferry dock, where you can catch the ferry across to Isla Mujeres.
You will get many opinions on where to stay and who to go out with. All I can tell you is what I did.
I stayed at the Rocamar Hotel, a short walk from the ferry dock in Isla Mujeres and quite centrally located, not far from the main town square. I highly recommend it, but if you are booking there, make sure to request a room that is at the same level as the front desk or above. There is a lower level - I would avoid rooms at that lower level because the patio door in those rooms opens onto a public oceanfront boardwalk.
I booked with Mexico Divers but they ended up sending us to a sister or affiliate company called whalesharkadventures.com.....ownership is within the same family. This is where it gets a bit complicated, because their standard itinerary is pretty much like the itinerary of most whaleshark tour outfits: leave at 9:00ish and come back around noon and spend an hour having lunch on the boat just off Playa Norte, the island's busiest beach. That's not what I had in mind because it doesn't give you much in-water time.
In my case, I chartered the boat with a group of friends for 5 days and wanted to maximize in-water time. To their credit, they were more than willing to accommodate us with earlier departure and later return times, foregoing the hour at Playa Norte, as well as picking us up and dropping us off at a dock close to the hotel. So from those respects, I have nothing but good things to say about them. But I don't know if they are going to do that for everyone, and if you are going by yourself and are just joining other "tourists", your experience may be entirely different.
Beyond that, there are outfits - wetpixel is one such outfit that comes to mind - that organize charter trips that cater to photographers and also strive to maximize in-water time. Needless to say, you may pay a little more.
Ultimately, the choice of who to go out with boils down to what type of itinerary is going to make you happy, and at what cost.
