1. Were you a good boy today?
This is the most correct question and most often heard.
2. Did you tease your friend today?
3. You were a good boy today, weren't you?
You can also use "have" ("Have you been a good boy today?" "You have been a good boy today, haven't you?"), but when you use "have" it means that the day or activity is not finished yet.
"Were" means the action or activity is finished.
For example, after school you want to ask "Were you a good boy today?" because you are asking about his behavior at school, which is now finished.
"Have you been a good boy today?" is a question you can ask if you take your son to the playground. You can ask this question while you are still at the playground because the activity isn't finished yet.
It is most common to use "were".