For a two-week trip, we like the 8-day Flex Pass for 467 CHF. It is a “choose your own adventure” pass, meaning you pick which 8 days you want to use it. We skip the days that are relatively inexpensive, such as a day of hiking from our base, and use it for the longer more expensive journeys.
Count up your travel and daytrip days and see if this makes sense. You may or may not want to include Zurich to Luzern, which is quite inexpensive, but maybe it fits within your 8 covered days.
Note that a Swiss Pass will fully cover Rigi but not Pilates.
Whatever you decide, you can buy it ahead if you like, or at the Zurich airport, or in Luzern if you want to pay for that journey and avoid spending time buying passes on your arrival,day, after the long flight. But compare prices, as often there is a fairly significant difference between the Rail Europe price in dollars, and the SBB price in Swiss francs. And consider whether your credit card imposes Foreign Transaction Fees.