Other than a few people who charter a boat they own or live on, there are only two main charter operations in Belize -- TMM in San Pedro and The Moorings in Placencia. There was a charter operation in Punta Gorda but last time I was there it was not operating.
If you have the time, you might want to split your trip -- part on a charter and part traveling around the mainland.
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