Yes, you can say both, and they mean almost exactly the same thing.
"What have you done today?" tends to refer to completed actions: "When I saw my friend this evening, I asked her: "What have you done today, and how many of those same things will you have to do again tomorrow?"
"What have you been doing today?" tends to refer to actions that are still ongoing: When I met my friend for lunch, I asked her: "What have you been doing today, and do you think you will get it all finished by the end of the day?"
However, if you exchanged "done" with "been doing" in my example sentences above, both would still make perfect sense; and be something that native English speakers say all the time.