I would probably split the time between Phyllis Dart's Ek'Tun Lodge on the Macal River in Cayo and Chan Chich at Gallon Jug, the first for the jungle setting, caving, and fantastic natural pool, and the second for the birding and wildlife spotting, plus Bowen's farm.
But there are many other good lodges: Chaa Creek, duPlooy's, Blancaneaux, Lamanai Outpost, Pook's Hill, Banana Bank, Jaguar Paw, Hidden Valley, among others.
--Lan Sluder