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.