They are all good. Each has different kinds of scenery. The scenery around Lake Lucerne ( der Vierwaldstättersee) is more varied than that around Lake Brienz (der Brienzersee) , and the lake is much bigger, so that there are different routes to choose from on Lake Lucerne.
Lake Brienz is almost completely surrounded by high mountains and does not have so much of the lower rolling hills that surround some of the northern parts of Lake Lucerne near the lake shore. The southern part of Lake Lucerne has more mountainous scenery. That part is called der Urnersee, because it is mostly in Canton Uri.
Lake Geneva ( Lac Leman) has varied terrain, like Lake Lucerne). Near Montreux, the mountains are quite high very close to the lake. Near genva and Rolle, the higher mountains are a bit further from the lake shore.
This link describes a hike near part of the Urnersee. You can get a good impression of the surroundings by looking at some of the attached images toward the end:
I don't have any images of the Brienzersee handy; I have taken many more photos around Lake Lucerne.
The attached images taken from a mountainous peninsula near Luzern give an impression of both the southern part ( toward Vitznau) and the northern part....toward Luzern and toward Weggis ( at the northernmost part of the Urnersee) and toward Zug and the Zugersee .
You can judge the lay of the land from this map:
By the way, keep an eye on the boat schedules:
On Lake Lucerne, they change on September 12th to a reduced Autumn timetable, and on October 24th, to a more reduced Winter timetable. Your trip should fit into the Autumn schedule.
I di not check the other lakes, but they also will reduce their schedules as the colder weather approaches.