Depends how you define "best" and also to a degree how experienced you are. AquaDives will probably be the cheapest and they have their own big boat for atoll trips, the largest on the island. Amigos have a gold-plated reputation and have a good boat for atoll trips, and will "do everything" for you. Both of these are large so may have more divers on boats, that that doesn't necessarily follow (especially at that time of the year, which is quiet). Against that there are several smaller operators which will give you a good personalised service - Steve's Ecologic Divers is probably the largest and busiest of these, then (in terms of size) ourselves, with Chuck 'n Robbie and Belize Diving Adventures (I hope that's right - I mean Everett and Enes) being very small but excellent. And you won't hear many/any complaints about Bottom Time or Patojo's.
Although most dive centers will pick you up at most hotels, you may prefer a shop that's close by. For that it obviously depends where you'll be staying. If you're not in town but are "up north" then several other operators come to mind.
You can maybe get some ideas from
http://ambergriscaye.com/ and
http://www.belizeforum.com/. Unless you're remote and effectively have little choice, I'd make enquiries now but don't book anything, then walk the beach once you're here and get a feel for the different operators - they're mostly not far apart. If you pay up front (eg. a package with accommodation) and then can't dive for any reason (health & weather are principle reasons), or just want to change operator, you probably won't get refunded for dives not taken.
As Steve said, not all dive centers are recognised by the training companies. This may not matter to you, but something to bear in mind. Also, although a real dive center has to have a boat and divemaster (there are some "booking shops" which don't even have that, but make their money on commission by booking you with an actual dive operator), quite a few don't have compressors or tanks but rent tanks from others. Again, may not matter. If you want to dive nitrox your choices are again restricted.