Seven Bridges near Tinseltown and Ragtime in Neptune Beach are both owned by the same people as well as a third restaurant in StAugustine. They have 4 or 5 house beers and they are not bad. The food is very good but a little pricey for me. Kickbacks in River side has the best beer selection in town. I have not tried there food yet though. No where else that I know of has a beer list like theres. Brewster's Pizza in Orange Park has a nice Craft Beer selection and great pizzas. They are starting there own house brew soon but I don't know when the first batch will be available. They do sell Growlers which are large jugs to go of any beer they have on tap. I have met the owner a few times and he is a true lover of good beer. The Ale houses scattered around town have a big selection main stream beers from around the world but nothing really I would consider "craft" beer besides Samuel Adams or Dogfish. Don't get me wrong, I like Dogfish. Hope this helps.
There are two "Breweries" in Jacksonville about a 100 meters from each other. One is called Bold City Brewery and the other is Inception Brewery. I don't know the exact address but you can do some google research and find out a bit more. The beers are ok and the atmosphere of each is great.