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.