Ferry service? Not really, but..
CMA CMG will be operating a shipping service between Comoros and Mayotte supposedly every 14 days.
The vessel is a cargo vessel, but it might be possible to hop on board as a passenger.
CMA CMG are known for accepting passengers on many of their cargo ships, so if you are flexible (and a little adventurous) why not check it out.
“”TRAVEL IN CARGO”” general information can be found on the VOYAGES EN CARGO Website: https://voyagesencargo.com
And the service in charge of quotations can be contacted via this Webform: https://voyagesencargo.com/informations-booking
The company have office / agent representative in all ports.