First start here - the official Belize Tourism site:
http://www.travelbelize.org/
You fly to Belize City then take a local airline - Mayan Island Air, Tropic Air or other local to San Pedro or anywhere else in the country. Besides Ambergris that could be the Hopkins area or the Placencia area further south. Assuming Ambergris Caye is where you want to stay/dive from - there's also a ferry. Caradonna lists a few packages on Ambergris -
Scuba Diving Vacations in Belize - Caradonna Dive Adventures
The better diving is off the Atolls but on most the dive resort is the only thing there. Most you'll travel via their transport once per week and stay there. So if you want to do any of the other eco-things on mainland Belize, Mayan Ruins, Cave Tubing, River tours, the Jaguar Preserve etc. you may want to find something on the mainland. I think there's options from Ambergris but I'm not familiar with that area. There's day tours from Placencia also.
Besides the Blue Hole, some of the best dives are at Turneffe Atoll, Lighthouse Reef and Glovers Atoll.
Some of the Atoll options are:
Belize Scuba Diving | Belize Flats Fishing | Belize Resort | Turneffe Island Resort
cocoplumbelize.com
Belize Vacation Resorts | Belize Honeymoon | Belize All Inclusive Vacation | Isla Marisol Resort | Family Vacations | Belize Tours
Caribbean Dive Resorts - Turneffe Flats - The Best Belize scuba diving resort - Turneffe Flats Belize
In the Hopkins area I only know of a few pricier luxury options. The reef is farther out there necessitating a longer boat ride out/less dives per day.
The Best of Belize Hotels & Belize Resorts | Welcome to Hamanasi!
Roberts Grove
Turtle Inn.
Still farther south in Placencia - Splash Dive bundles packages with several local resorts in all price ranges. Same longer boat ride out as from Hopkins - usually means 2 dives/day plus an optional night dive. There's no shore diving there, it's too flat. Some friends recently did an affordable trip with Splash staying in a decent local hotel nearby - booked it all thru Splash. We had planned a trip there last year and liked the looks of this place - affordable, beachfront and they package thru Splash also.
Laru Beya - Placencia Belize Resort
Belize Scuba Diving Packages, Snorkeling & Whale sharks|Splash Dive Center|Placencia Belize
Avadon Divers Belize
Late spring the draw in Placencia is diving with the Whale Sharks off Gladden Spit. It's only certain weeks during/after a full moon when the Cubera Snapper spawn. Either operator ^ has dates/details on their site.
I moved this thread to the Belize sub-forum...