I use San Pedro-Belize Express and like it. It's drops you within a block of Mirab (shopping mecca) and carries quite a lot of goodies home for you free of charge.
It is the newer of the two services. Cant' say if it's "better" than Caye Caulker Water Taxi. My guess is that they are similar.
The two seem to be pretty full most of the time, and have worked together to stagger arrival and departures so as not to create any dangerous traffic.
They depart from locations that are quite far apart (in San Pedro) giving reasonable access to folks living in different parts of town.
Sorry to see them in a fight!