Treasury Software has been mentioned in this thread. I've been using it for several years with QB desktop with good results. I recently moved to QB online and it works with that too.
It works by taking the payments information from QB and creating a file that can be uploaded to the bank. It's about CAD$25 per month to use. The only issue is that it's an American company. It definitely works with Canadian banks, but the setup is a little complicated. I recommend contacting their support team and getting them to help set up. It's simple to use once it's setup, though.
Another option is a company called Telpay. It's a Canadian company, so it would probably be easier to setup. I don't have any experience with it, but I think it might be cheaper overall because with Treasury Software you have to pay bank fees in addition to the Treasury Software subscription.
Note: I have no affiliation with Treasury Software, Telpay, or Quickbooks/Intuit. I'm only a user.
