Wow! That is a loaded question. You will find that the majority of builders have several locations in Northeast Florida. There are custom builders that are pretty much high end, then there are some pretty good small builders , not part of the big boy network that give a quality product for less that 225K. In the past few years, the buyer's final walk-through inspections for all of my clients have been relatively trouble free with everything in good order.
As a member of the Realor communiy it would be unethical to say bad things about any of the local builders in a public forum. I can assure you, if you have specific questions about any particular builder or can be more specific as to what "best" builders means to you , I wll do my best to answer honestly any questions you might have if you would like to contact me at firstname.lastname@example.org or call me at 904-635-4766. I will be more than happy to answer your questions with no obligation attached.
As with most major cities, Jacksonville has a number of national builders as well as a number of local builders. The big national firms are rated by JD Powers and it's easy to look them up and pick amongst them. The local builders are a little more difficult to judge and for every bad story you hear about a builder there are typically just as many good ones. Everyone has a bad day or makes a mistake once in a while, so the real question is how well do they handle their mistakes and how is their customer service rated. It's pretty much the same as any company that sells it's end product to the consumer.
The key, really, is to select the area you want to be in and see what builders are in that area and then selct the best among them. When they are pretty much equal in terms of quality and customer service, the value they offer in that particular development vs another builder will be the determining factor.
Depending on your price range and what you need in a house, some of the local custom builders could do very well for you on your own lot..
So, Cathy has a good point. Your question needs to be qualified further and the answer to your question really is so subjective that it's tough to get an easy answer. Good Luck.