The airlines direct website booking is usually cheapest, but you can use Travelocity to compare which airline is lowest. I never book with Travelocity, just use it to see who is offering the lowest fare and sometimes which airlines even fly to the destination I am looking at. Then deal with the specific airline.
I have seen SFO to BZE for under $350 at certain times of the year. You just have to keep watching on an almost daily basis to catch fare sales. The Taca website has a feature you can use that will e-mail you when they run a sale to a destination you are interested in. American releases sale prices on Tuesday mornings and also has an e-mail feature.
I am flying Taca in 10 days - SFO to Roatan and then on to Belize using frequent flyer miles all booked through American. I didn't bother to check what the normal cost would be as they had availability with my miles.
In some cases if you book the trip in separate legs, using a regional airline like Southwest for example, you can save several hundred dollars. It does take time and effort. If you don't enjoy doing your own research, find a travel agent with experience in the area you are traveling.
* And remember it is cheaper to fly mid-week.