Thats a tough choice there are pros and cons to both for sure. NRT is a long way from downtown Tokyo, but I'd much rather fly with ANA over AC. That being said HND is so much closer to downtown. In your case I think I would pick the arrival into HND even if it means flying Air Canada. I think I would worry to much about the 90 minute connection to the last train to much. Although I know there are buses that are cheaper, but I don't know the details as I have only taken the train.