If you are going to do a Shore Excursion, then I would book with Carnival. That way you have a guarnetee if something goes wrong. For instance, the Estascy was 2 hours late into Cozumel when we went a week or so ago, those who had booked SE w/ Carnival were taken care of and the tour waited or it had to be cancled they were refunded. Also, if you are on a tour booked w/ Carnival and they are late to get you back to the ship then Carnival will wait for you.
I did not do any SE's when I was there but after a LOT of research I would only book w/ Carnival and pay that extra instead of relying on a tour group that does not have alliances with Carnival.