Will I be allowed back into the US if I go from Canada to Chicago (26 September), back to Canada and then Canada to Cuba (29 October to 5 November) back to Canada and then Canada to New York (28th December to January 2nd)? Does Cuba reset the 90 day count?
Short and bitter: No, it will not, because Cuba is considered an Adjacent Island for Visa Waiver Program purposes.
However, if you're Canadian or resident in Canada, returning to your place of residence does reset the clock.
In law, the islands are listed specifically:
The term “adjacent islands” includes Saint Pierre, Miquelon, Cuba, the Dominican Republic, Haiti, Bermuda, the Bahamas, Barbados, Jamaica, the Windward and Leeward Islands, Trinidad, Martinique, and other British, French, and Netherlands territory or possessions in or bordering on the Caribbean Sea.
You propose to spend 33 days in the US, return to Canada, travel to Cuba, and return again to the US 93 days after your first arrival.
It doesn't really matter; your first 90 day admission stamp would have expired anyway when you arrive in the US the second time. You won't qualify for automatic revalidation. So whether you travel to Cuba or not is irrelevant.
Here is your official reminder:
When traveling to the U.S. with the approved ESTA, you may only stay for up to 90 days at a time - and there should be a reasonable amount of time between visits so that the CBP Officer does not think you are trying to live here. There is no set requirement for how long you must wait between visits.
Occasional short visits are fine. The intention is to prevent "visa runs", not to catch out tourists who are a little uncertain about "the rules".
At the border the second time, you should expect some questioning about what you were doing in Canada and Cuba, and you should be able to explain confidently. Aside from that I see no real issues with the itinerary.
Doesn't matter. Let me repost the image from https://travel.stackexchange.com/a/61835/4188 to show you a rule of thumb where you need to be out for 91 days after being in for 90: