You have this pencil too, don't you? is correct. Why? Because it indicates ownership in the present. "Have" can also be used to construct the Present Perfect Tense; so your sentence would then be: You have owned this pencil too, haven't you? meaning that the person owned the pencil in the recent past.

The first option - 'haven't you?' - isn't wrong. It is just very outdated and odd-sounding in modern English. Just as nobody says "Have you a pencil?" nowadays, nobody would say "You have this pencil, haven't you?". In modern English, we usually treat 'have' like any other verb, and make questions, negatives, short answers and tag-questions with the auxiliary 'do'. This is why we say "You have this pencil, don't you?". Note that one exception is when we use the 'have got' form. When we add 'got' to the mix, we do treat 'have' as if it were an auxiliary verb. For example, "Have you got a pencil?" "Yes, I have"/"No, I haven't". Following this same pattern, we use 'have' as the auxiliary verb in tag questions: "You've got this pencil, haven't you?" "You haven't got this pencil, have you?".

The 2nd one, "don't you" would be more accurate. The first one is not correct. You could also just use the word "right" or "correct." You have this pencil too, right? You have this pencil too, correct?