Tough call.
The Fire dungeons are indeed some of my favorites, always ranking as one of the top ones in each game. That said I think Wind Waker's Dragon Roost Cavern is the lesser of the fire dungeons, even if it's quite a good dungeon. It's a bit simple and has no mini-boss, but maybe I should excuse those since it's Wind Waker's first dungeon. To me though it comes down to Ocarina's Fire Temple, Twilight's Goron Mines and Skyward's Fire Sanctuary.
I thought the latter was was very clever, but it ruined it with one thing: the leap of faith at the end that was spoiled by a stone tablet at the beginning which would've been more fun to figure out yourself. Goron Mines is original because it's not truly a dungeon, has a small side-story inside and comes with a good set of puzzles. Sadly though it's boss is one of the weaker ones in the game.
Leaves the Fire Temple. I think this one is all-round the best one, has an awesome boss even if it's a bit on the easy side and is very consistent in it's theme and is cleverly designed around the imprisoned Gorons and the tall central pillar.