Is the amount of water going over Niagara Falls very different in September compared to summer?

The flow over the falls is influenced by the hydroelectric power plants in the region. However, by international treaty, the flow is maintained at a certain minimum amount:

The 1950 Niagara Treaty established minimum flows over Niagara Falls for scenic purposes. Note that Niagara Falls refers to the sum of the flow over the American and Horseshoe Falls. The Treaty states that the flow over Niagara Falls should not be less than 2832 m³/s (100,000 ft³/s) each day between the hours of 8 a.m., E.S.T., and 10 p.m., E.S.T., during the period of each year beginning April 1 and ending September 15, inclusive; and each day between the hours of 8 a.m., E.S.T., and 8 p.m., E.S.T., during the period of each year beginning September 16 and ending October 31, inclusive. Falls flow should not be less than 1416 m³/s (50,000 ft³/s) at any other time.

So as long as you go by the end of October, and there isn't a drought on in the Midwest, then you should get the full effect. The flow is generally higher when Lake Erie levels are higher, and right now water levels in Lake Erie are about 0.4 m above their seasonal average. (Note that the historical range of data only spans about ±0.75 m.) There's no guarantee that the lake levels will be higher next summer than they are right now, so I wouldn't take the amount of water going over the falls as your determining factor.