There are now scheduled water taxis leaving from TWO locations in Belize City -- the old Marine Terminal next to the Swing Bridge and the new Fort Point Tourist Village docks. Most visitors seem to prefer the new Tourist Village location, as it's clean, safe and more user friendly. The Village has about 30 shops including some restaurants and a cybercafe.
I'm not sure if Thunderbolt is now a part of this new Water Taxi Association or not, but in any case there are plenty of boats.
Here is the schedule for the Tourist Village boats, which was posted by someone else recently (Silkpainter). The Caye Caulker Water Taxi Association boats from the Marine Terminal have a somewhat similar schedule. That's posted somewhere around here. As I recall leaving from Belize City it's 9, Noon and 3 most days. Prices are the same from either place.
Tourism Village Water Taxi Association Schedule
9 boats, some are partially covered
Water taxis will stop at St. George’s Caye and Caye Chapel to drop off and pick up passengers on request. Call 226-0232
The Tourism Village has a brand new terminal at the mouth of the Belize River with plenty of free parking for taxis, busses and autos. Clean bathrooms – no charge.
Belize City to Caye Caulker
One way - $15 bz. per person
Round trip - $25 bz. per person
Travel time approx. 1 hour
Belize City to San Pedro
One way - $25 bz. per person
Round trip - $45 bz. per person
Travel time approx. 1-1/2 hours
Departs from San Pedro Texaco Marina stopping at Caye Caulker and arriving at Belize City Tourist Village
Dpearts from Caye Caulker Municipal Dock on the back side of the island and arrives at Belize City Tourism Village
Belize City Tourism Village to Caye Caulker & San Pedro
4:30 p.m. (last boat that goes all the way to San Pedro
5 p.m. (to Caye Caulker only)