I'm almost certain that Monkey D. Dragon has either one of two devil fruits.
1. Wind Wind Fruit or something wind-related | Logia: Remember in Loguetown/Roguetown when Dragon said "Wind Blast"? I bet he has some kind of Logia fruit that controls wind.
2. Storm Storm Fruit or something weather-related | Paramecia: I believe this one more. He can control weather. He could still do "wind blast". Do you really think a lightning bolt suddenly appears and hits that spot??? There was plenty higher places there!! And it starts raining exactly when Mohji is gonna burn Going Merry/Merry Go. Plus, the wind was blowing in the direction they were headed. The rain also wet the navy/marines gunpowder so they went to get more, leaving the way to the ship ungaurded. Come on. Its easy to see its one of the two, (most likely this one) but Oda hasn't saids nu'in.