Western Fairy Island
Use the Skull Hammer on the nearby post to make the fire barrier disappear.
Thorned Fairy Island
Use the Skull Hammer on the three obstructing posts to enter.
Northern Fairy Island
No special items are needed; just walk on in!
Use the Wind’s Requiem to make the wind blow to the West. Walk up to the bridge area that leads to the Forest, then turn right and follow the path. At the top, climb up onto the rock that’s closest to the island, then jump off and deploy your Deku Leaf. Once on the other side just navigate through the forest and bomb the lone boulder.
Eastern Fairy Island
Use a bomb to blow up the obstructing boulder.
Southern Fairy Island
Shoot a Fire Arrow at the wooden boards to burn them away.
Mother and Child Isles
Use the Ballad of Gales to warp inside of this otherwise inaccessible island for the Fire and Ice Arrows.
Defeat Phantom Ganon to receive the Light Arrows. Not strictly a Great Fairy, but pretty useful!
Look for the flock of seagulls, then sail there to engage a 4-eyed Big Octo. Take out all his eyes to release this Great Fairy.