It means "Are you eating enough fish each day?"

A "quota" means "the minimum amount you need to have." In corporations salespeople might be given a "sales quota." A monthly quota of a million dollars would mean they're expected to sell a million dollars worth of something every month. "Have you been getting your daily quota of fish" means that someone believes it is necessary for you to eat a certain amount of fish every day. That amount is your "daily quota." Thus, as Mark says, "have you been getting your daily quota of fish" means "have you been eating enough fish?"