I'd say, "how long will it take?" or "how long will it be?" However -- this is also the phrase you'd use if you are impatient and cannot wait. If you say it with an unhappy face, the cashier will probably feel like you're giving them a deadline, instead of simply asking for an estimate. To soften it a little you could say, "when can I pick it up?" or "when do you think it will be ready?"

When will my order be ready ?

"How long will it take?" would be what most people would say.