Rob gave you good advice. The issue is that crossing the border in the Niagra Region (Peace Bridge, Niagara or Queenston/Lewiston) will put you smack dab in the sights of having to get by Toronto.
Let's make this clear. The 401 is the busiest Hwy in North America. Busier than New York, Los Angeles or Chicago. Think transports, idiot drivers and construction. By most normal peoples traffic standards it's ALWAYS rush hour. Any time between 7am and 10am and 3pm and 7pm, it's a parking lot. Not a good place to be on a bike!
If it all possible, I suggest crossing to the East of Niagara. Thousand Islands, Ogdensburg or Cornwall. (oh, btw, Ogdensburg is a VERY tall metal grate bridge just so you know). Once you get outside of the Toronto vicinity, riding is much better, at least as far as traffic/roads are concerned.
BTW, I think paying the toll on the 407 is worth the money to avoid the 401/427 corridor. MUCH less traffic even during peak times. So it costs you $15 one way. Your around Toronto in 15 minutes instead of 60-90 minutes.