First off, the "too chatty" flag really sounds like it is meant for comments that have diverged into a side conversation. If anything, "joke" comments would fall under "Non-constructive", as they really are not helping improve the question/answer.
We definitely don't want to go the #3 route, as that would require our moderators to suddenly become the final arbiters of what is or isn't funny, and we all know @Richard has no sense of humor or spelling.
For normal users, I think this is just one of those things where we leave it up to the user to decide for themselves. I don't see any reason to tell users to actively flag jokes (the way we are asked to actively flag spam, dupes, etc.). But, at the same time, I don't think we can really say that humor is sacred and we must never flag a joke. If I don't mind them, I won't be bothered by them. It likely even depends on the exact questions at issue: Doctor Who fans are more likely to play fast and loose with humor than some other fandoms because the show itself is extremely humorous.
As far as moderators are concerned, though, there isn't much room for debate. The purpose of comments is to help improve the questions and answers, and jokey comments (that don't also serve that purpose) are off-topic. They are non-constructive. I think there is a benefit to them as they make the questions and answers more enjoyable to read, but strictly speaking, they don't make the questions or answers any better. Since that is ultimately the reason that all stack exchange sites exists, I don't think there's any justification to change that policy just to keep more humor around.