Niagara works best if you are interested in touring wineries. The only decent hike is the one down the gorge to the river at Niagara Glen Park. There are some other parks and nature reserves but you will need a car.
Toronto sprawls and sprawls; it's hard to find good outdoor areas that are accessible from the city and definitely you won't find anything accessible by public transit. But, nevertheless, there are some larger parks with trail systems right in the city. Have you been to the zoo? It's fantastic and very large. Right next door is Rouge Park, which is a giant natural area within the city's boundaries. Have you been to Toronto Islands? You might enjoy biking on the Islands. Tommy Thompson Park on the Leslie Spit is another wilderness-like area that is located in the heart of the city.
Perhaps you could base yourself in Peterborough - a nice town that has some "nature" areas close by: Warsaw Caves, Petroglyphs Provincial Park. You can take a bus to Peterborough but once there you will need a car to explore outside the city.