As for coming from Toronto, you have several options to get to the US. 2-3 days is not unreasonable to get to Niagara Falls. Follow the Waterfront Trail. Another option is to use the GoTrain Excursion trains from Toronto to Niagara falls On, these run Friday night, Saturday and Sunday and holidays thru September. The excursion train allows one to roll the bike on to the train.
As for crossing the border in Niagara Falls area, you can use the
Peace Bridge in Buffalo/Fort Erie, this bridge you cross using the pedestrian sidewalk, there are signs on the road under the bridge on the Canadian side for pedestrians and cyclists.
The rainbow bridge in Niagara Falls, you cross with the cars and enter from the street, the sidewalk is closed to bicycles.
The Lewiston-Queenston bridge in Queenston/Lewiston, on this bridge you cross with the cars and the bicycle entrance on the Canadian side is under the bridge on the Niagara Parkway, there are signs It requires you to go thru the parkinglot for the bridge offices and then cross the traffic into Canada between the Customs booths and the Toll booths and then merge with the US bound traffic. After the US Customs inspection you take the first exit ramp and then the first exit onto Lewiston RD RT104. The Canada bound route is to take the on ramp at Military RD/Upper Mountain rd to Canada and then at the toll booths in Canada take the right most open toll booth as you will then hop onto the sidewalk on the toll boths and follow the sidewalk around to the right and the parking lot for the bridge. Do not go straight after the toll booths as you will be on the QEW!
The whirlpool bridge is closed to all traffic except cars and everyone in the car must have the NEXUS card including any children. Even if you have a NEXUS Card, the Whirlpool bridge is closed to cyclists.
I would suggest using the Rainbow bridge as being the most bicycle friendly/accessible.