Here is our plan for a complete visit to Niagara Falls which takes one day by bicycle. Alternatively, you can walk the Falls part and then drive to the Rapids and Whirlpool. 

Park at the free parking lot on Goat Island. Ride and walk along the southern shore of goat island to Terrapin Point. Then to Luna Island to see Bridal Veil Falls. You'll have to carry your bike down some steps to get to Luna Island. Then return to Goat Island and follow the trail to the Bridge to the mainland and ride along the shore to the American Falls Overlook. You will need to walk your bike at the crowded viewing areas. 

When finished on the American side, ride your bike across Rainbow Bridge. The traffic will be stopped or moving very slowly so there is little danger in this. You can go right to the front of the line and pass through immigration on your bike. The last time we did this, the toll for pedestrians and bicycles was ten cents. (Remember to bring suitable documentation to prove your citizenship.) On the Canadian side, follow the road upstream beyond the Horseshoe Falls. Then walk your bike downstream along the promenade to observe the falls. When you are finished with the falls, you can follow a bike path along the Canadian side to the Lewiston-Queenston bridge (6 miles) and return along the American side to your car (about 8 miles). You'll have great views of the Gorge, Whirlpool, and power plants from the frequent overlooks.