On our ride from Burlington to Niagara, we took the train from Toronto to Burlington and we ended our Bike Tour at the Niagara GO Station, where we took the train back to Toronto. Sorry if this is cheating, some day I will be able to make the ride from Toronto to Niagara Fall ad come back on the same day purely on my bike. Oh, almost forgot, we paid a promotional fare for unlimited day rides on GO, valid on weekends and holidays.
We did another cool trip starting with a GO trip from Toronto to Niagara Falls, riding to Niagara on the Lake and taking the GO Train back from St. Catharines. Wanted to leave it here as an inspiration for others.