EDIT: I realized the the note examples look confusing, so I clarified them somewhat.
Depending on how familar your sister is with Disney movies.... you could BUY a Disney movie that has a godmother in it of some sort... Sleeping Beauty has the 3 fairy godmothers... Cinderella has a fairy godmother... I'm sure there are others but I'm drawing a blank... give her the movie as a gift (xmas, maybe?) and inside the case of the movie... put a note that says something like:
"Dear Aunt (sisters name), in this movie, (character's name) has a wonderful fairy Godmother. I need a wonderful Godmother, too, and the first person I thought of is you! Love, (son's name)"
Alternatively, you could do the same thing but make the request from you (and your husband if you are married) with a note that reads something like:
"(sisters name), As I was thinking about the story in this movie, I couldn't help noticing that (character name) has a very special fairy Godmother. I think (son's name) deserves a very special Godmother, and I would be very honored if you would be his Godmother. Love, S.."
- if using Cinderella, character name would be Cinderella. If using Sleeping Beauty, character name would be Aurora, and the wording would be changed to reflect three godmothers.