Rheinfall and Lindt Museum on the same day? That’s quite challenging, time-wise.
Day 1) You could buy a return ticket Kilchberg to Schloss Laufen. It comes as a day pass and also includes the Zurich city (zone 110).
Day 2) Simply buy Zurich HB to Pilatus Kulm ticket.
The 22 and 16 years old need also adult tickets (full fare). The 13 years old could buy a Day Pass for Children for CHF 19 / day.
I suggest you to go to the Zurich HB ticket office and tell the colleagues at the ticket counter where you want to go; they will sell you the right ticket. There is no need to buy tickets in advance.
Going by car is not an option. Zurich and Lucerne are anti-car villages with high parking fees. And, Mt. Pilatus is not accessible by car.
Alternatively, Mt. Rigi would also be possible. With a Saver Day Pass, starting from CHF 52, you could do a round trip: Zurich HB - Arth-Goldau - Mt. Rigi - Vitznau - (Lake Lucerne boat) - Lucerne - Zurich HB.
The TripAdvisor Switzerland forum and myswissalps.com are travel forums run by locals who can help you to plan your trip, although your trip by plane it is too short in my opinion.
Here, we remain at your disposal for any ticket questions.