The route between Niagara Falls and Niagara on the Lake is a no-brainer: follow the bicycle path next the Niagara River! What you do next... well, that depends on what you want to see. I have taken quiet back roads past orchards and vineyards from Niagara on the Lake until just north of Niagara Falls. All you need is a decent map to find your way. You can head west from Niagara on the Lake along the Waterfront Trail and follow the shoreline of Lake Ontario. It loops around the western end of Lake Ontario and continues east all the way to the Quebec border. Obviously, that would be too ambitious for a two day trip! But if you follow the Waterfront Trail west, I suggest leaving the trail and going south until you hit the wine route, and then continue west. The climb up the Niagara escarpment is intense, but the roads on or near the crest are gorgeous for bike touring.
A two-day circle from Niagara Falls might look something like this:
Day 1: North along the bike path from Niagara Falls to Niagara on the Lake, west along the Waterfront Trail until you cross the Welland Canal, wiggle north and west to the Wine Route, and then west to either St. Catherines or Jordan.
Day 2: Wiggle south and east back to Niagara Falls.