For Toronto to Montreal you can't get more detailed directions than this:

http://www.hedney.com/waterfront.htm

Its not the most direct route but its very pleasant. I've followed his route as far as Brockville. Bloomfield Bicycle company is supposed to be a wonderful lbs if you need anything, I didn't get the chance to check them out but heard many good things.
For Niagara Falls I'd try the waterfront trail route.

From Science Center easy take the Don trail down to the waterfront although annoyingly the connection is closed right now and you don't want to take a loaded touring bike up the stairs at Queen Street. There's a hole in the fence on the Don trail that will take you out onto the Bayview extension, from there turn onto Queen Street east or west depending on which way you are going - if east I'd take Queen all the way to Kingston Road, the short stretch of waterfront trail left is not worth the detour. If west left on Sumach, turns into Cherry down to the wft.