When I saw the episode I never felt it had anything to do with IT. I think you can always draw comparisons between films, but this didn't feel like a direct reference at all.
Mr. Chuckle Teeth is also a toy based on a children's tv series, which is something completely different from IT.
Mister Chuckle Teeth
EDIT: well, it seems in the trivia section of that link IT is indeed mentioned and the episode as having similarities and homages to IT. So the OP was probably right, although it didn't feel to me that way. I'll probably watch the season again in some time and see if I can spot the similarities.
The season overall was better than the first revival season, but the storyline of Mulder and Scully's son didn't amount to much in the end unfortunately,