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There are many ways of achieving the levitation effect (potions, spells, etc.), but you can also achieve it by cheating. Use the console. If you're on a computer, Press [~] (under [Esc]) and then type TCL and press enter. If you don't want to cheat, you can enchant a piece of clothing with levitate (or the ability to breathe underwater), and put it on when you want to fly. When I played through, I enchanted one shirt to make me levitate, and one that would let me breathe underwater, so I could explore underwater ships and also get into places that were impossible without flying.