I am paraplegic and want to swim with whale sharks. Which operators have experience with such cases?

Check out the Diveheart organization. They specialize in adaptive scuba diving and snorkeling for people with disabilities, including paraplegics. They might be able to connect you with an operator in Isla Mujeres that can accommodate your needs.

I'm not sure if it's relevant, but I wanted to let you know that whale shark season in Isla Mujeres is usually from mid-May to mid-September. This year's window has already closed, so you might want to plan ahead for next year.