Why don't you take a cruise? The highlight of the Yangtze River is to view wonderous scenery of the Qutang Gorge, Wu Gorge, Xiling Gorge during the cruise. It's hard to give you an appointed place.

If you just want to see the Yangtze River you only need to visit one of the cities on the river like Shanghai, Wuhan, Yichang, Chongqing.

However if you wish to see the three gorges area then you really need to visit Yichang and take either a two/three days cruise to Chongqing or visa versa. Another option is to take the hydrofoil from Wanzhou to Yichang and back again or continue by bus to Chongqing.

As far as I know the hydrofoil cannot travel to/from Yichang these days. A bus takes passengers from the city to the dam (about 30 miles upstream) where the hydrofoil now effectively ends.

Hope this information is helpful