We have golfed quite a few of the Orlando mini golf courses. Here is our ranking, in order of overall preference (best to least) taking in theming, cost, and all other factors:
Congo River (love being able to also feed the gators and turtles!) - multiple locations
Hollywood Drive In Golf - Universal CityWalk
Pirates Cove - multiple locations
Mighty Jungle - Kissimmee
Gator Golf - International Drive
Hawaiian Rumble - I-Drive (also has a course in Lake Buena Vista)
Volcano Island - I-Drive