Both are correct. In a phrase of -고 싶다 and the verb is a transitive verb, the particle '이/가' and '을/를' are interchangeable each other. The meaning does not depend on '이/가' or '을/를', but depends on the context. Here '이/가' is used not as a subjective particle but as an auxiliary particle.

Both are correct, but generally you'd see a sentence like the first one used. The second one really emphasizes what you want to eat - 사과. 1. I want to eat an apple./I want to eat apples. (General) 2. I want to eat the APPLE. (Specific or emphasized, less broad)

Both are correct :)