Upvote:5
You and your son both carry Canadian passports. Unless there is some unfavorable circumstance such as a criminal record, Canadians do not need a visa for transit through the US (or indeed for most other purposes). As long as the traveler presents a Canadian passport, it does not matter what other citizenship may be held or where the traveler was born.
Canadian citizens also have a right to enter Canada, of course. Therefore, to answer your question:
Do we need some sort of special permission if I want to travel to Canada with a connecting flight through the United States?
No.