If you’re still experiencing issues getting to the Dragon Isles from Stormwind Harbor, here is a potential fix for the issue.
Apparently, the boat spawns on the right, in the ocean/fatigue zone, and if you wait near the edge and get the timing right, the boat will spawn on you, instantly completing the state of the quest that takes you to the Dragon Isles.
The tip comes from Reddit user YeahDaryl who provided the following map. The golden pin shows where to fly when the boat is about to spawn.
Boat timers are displayed right above the Dock Master’s head.