Elena is absolutely right about the general rules.
1) it is true that he is the wisest, isn't he? - means we are still not certain whether he is the wisest. The whole statement is positive, so we need to add the negative tag. If the question is about him being wise, we should use "he" in the tag.
1) it is true that he is the wisest, isn't it? - If we are uncertain if it's true or not, we should use "isn't it".
It can be read both ways.
2)I don't think he will come, will he? - means our uncertainty about him coming. The sentence is negative, you don't think he is coming, but still are uncertain about it. So the tag should be positive.