In the chapter titled "Signlight and Moonlight" there is this paragraph: “I want some gum-drops,” she said, humorously apologetic; “you can’t guess what for this time. It’s just that I want to bite my finger-nails, and I will if I don’t get some gum-drops.” She sighed, and resumed as they stepped into the empty elevator: “I’ve been biting ‘em all day. A bit nervous, you see. Excuse the pun." I am not a native English speaker and I do not understand the pun in here. In Chapter II (Symposium) what's the meaning of "unpleasantly undergraduate" in the phrase "the best of the men not unpleasantly undergraduate"? Further on when Maury speaks of himself he says "I read Smith, who laughed at charity and insisted that the sneer was the highest form of self-expression–but Smith himself replaced charity as an obscurer of the light." What exactly does the author mean by obscurer of the light?

In terms of the pun in the first quotation, I cannot be entirely certain without seeing the full context, but I would interpret this to be a joke on the part of the author—that is, there is not actually a pun at all. A phrase like "Excuse the pun" might be dropped into conversation by a nervous person almost as a figure of speech, without this person having actually made a pun. The joke is therefore that, whatever pun the speaker is thinking of, it was not evident to the listener. It is entirely possible that the pun could be on "gum-drops" and nail-biting—with "gum" here referring both to the gums in the mouth and the gum that the drops themselves are made of—but this is extremely tenuous and not truly a pun.
"Unpleasantly undergraduate" is an interesting one; "undergraduate" is here being used as an adjective, but it is typically used as a noun. If someone is "unpleasantly undergraduate" that means that they are behaving unpleasantly like an undergraduate (a student who has not yet graduated from university). As a result, an "unpleasantly undergraduate" person is immature in the manner of someone aged between 18 and 21 and probably has some mannerisms particular to a college student (pretentiousness, an inflated sense of self, and so on).
In the third example, "obscurer of the light" would literally mean someone who gets in the way of the light. In this case, it is probably being used metaphorically: an "obscurer of the light" is someone who makes it difficult to see or understand things clearly, or, alternatively, it could refer to someone who makes it difficult for goodness to shine through.