I would definitely go for one of the boats from Calis.
Not having to traipse to Fethiye first thing is a big factor, and the transfer isn’t free - Fethiye boats trips are more expensive.
We’ve also found the food better - typically 15 mezes, barbecued chicken and kofta, with cake and fruit in the afternoon. The ones we’ve been on from Fethiye have had a ‘queue up and be served’ system, which we hated, whereas on the Calis ones, everyone sits round a big table, and the food is put on the table for people to help themselves.
Our favourites are Alis boat and Ekinim, mainly because we’ve used them a lot, but friends love other Calis boats. They operate as a cooperative so have similar standards.