There are 3 water taxi services between Belize City, Caye Caulker and Ambergris Caye (see websites for schedules & fares).

a) Caye Caulker Water Taxi Association:
http://www.cayecaulkerwatertaxi.com

b) San Pedro Belize Express Water Taxi:
http://sanpedrobelizeexpress.com/index.html

c) San Pedro Water Jets Express:
http://www.sanpedrowatertaxi.com/index.html

The Belize City terminals for the CCWTA and the SP-Belize services are very close to each other in Belize City -- both a short walk from the Swing Bridge. The SP Water Jets terminal is at Bird's Isle, at the other end of the City, about 1 km from the Swing Bridge.

The SP-Belize service has a very nice waiting area in Belize City terminal, but the CCWTA terminal has been upgraded since I last saw it.

Your decision might be based on whichever water taxi departure fits into your travel plans.