The game refers to Webber using "it" pronouns at the end of adventure mode.
Webber generally uses "we" instead of "I", and "us" instead of "me". He mostly only uses "I" when referring to past experiences as a human. "We could be good at football, much better than I was!"
The only other time that I am aware of that mentions Webber's pronouns is the description of Webber's Skull, which uses "he", and the DLC description, which uses "he" to refer to the person who got eaten by the spider to form Webber. The skull is human, so it's likely that Wilson is referring to the one who got eaten by the spider, especially since Wilson doesn't know who Webber is. Since the other characters don't know Webber, their comments don't really count.
Also, Webber can lay eggs, which I guess ought to be mentioned. The spider is female.
Seeing as the game is set to use "it" for Webber, and Webber uses "us", I think it would be more appropriate to use "they" or "it" to refer to Webber, and "he" when referring to the boy who got eaten to form Webber.