Wow, tough questions... kind of like what's the "best" flavor of ice cream....
I will try to give you my admittedly biased opinion..
I like the general area of High Springs, due to proximity and options for food and shopping. Close to Gainesville etc.
As far as shops, I like both Cave Country Dive shop and Amigo's for different reasons.
Cave Country would get my recommendation if you need a full service Dive shop with full support and the "normal" retail experience, plus all the cave/tech stuff you could ever hope for.
Amigo's is all together different. Mostly self service, and a lot of flexibility. If you catch Wayne on site, you can be sure to feel like family within a few minutes. I like this place for the atmosphere. If it's not blazing hot, you can often find both locals and visitors around the campfire in a very relaxed setting.
Accommodations will depend a lot on what you need as well. There are not many high end options close by, but there are options. Several options for rental rooms, houses, or trailers perfect for divers. There are even a couple of the local dive shops with inside contacts that will get you in contact. I would just say to make very sure you have a solid reservation with dates and specifics. I have heard a couple bad stories of people showing up that had to "share" a house, whe. They were expecting a more private experience.
I don't like to recommend instructors, because it's just way to personal. I would just say there are a couple great options that post regularly here. Do your homework!