They are both sharp pains, though appendicitis can start as a cramp feeling first. One is higher than the other. The cyst pain will appear during ovulation, at least that is when it is at its worst. Both need to be looked asap. Not all cysts are created equal. Some need immediate attention. Appendicitis also can't wait. Better safe than sorry. Get it checked out.
The only way to know for sure what is wrong is to go to the doctor and have an MRI or CT scan. That will give them a better idea of what is going on. No one can know for sure what is going on, but that will give them a better idea.