As a general rule in Belize, you'll get a better rate by booking direct with the hotel, especially via the Internet. Most properties in Belize are small and don't like to pay travel agent or wholesaler commissions (though of course they won't say that in public or to travel agents.)
There are some exceptions. Sometimes agents will have negotiated an especially good price and can offer rooms for less than the hotel quotes direct. That's particularly true of agents who are in Belize or who specialize in Belize travel. Also, sometimes wholesalers or packagers such as Capricorn Travel do air/hotel packages that are lower than you can put together yourself, although in most cases you are limited to only a few hotels.
Finally, off-season sometimes walk-in rates are the lowest rates of all. Just show up and shop around ... but you take the chance that the hotel you like is full or isn't willing to do negotiate (or that whoever is at the desk doesn't have the authority to do deals).
Belize books and publications by Lan Sluder:
Belize First Magazine (http://www.belizefirst.com
Fodor's Belize & Guatemala Guide (new 4th edition coming this summer)
Adapter Kit: Belize (the first and only comprehensive guide to living, retiring, working and investing in Belize -- a best-seller on Amazon.com)
San Pedro Cool (the first and only visitor guide to Ambergris Caye)
Belize First Guide to Mainland Belize
UpClose Central America
Belize Book of Lists