I know of no discount with a Swiss pass for the German part of that route. Walk up price in Munich would be €38-45 per person, depending on the class of train you take. That would be for a German Rail ticket to the first station in Switzerland (St. Margrethen); your Swiss pass would be valid from there, although you might have to get off the train in St. Margrethen to have your pass validated by Switzerland.
There are discount tickets available from the Bahn, but they are advance purchase, train specific, non-refundable, so you would risk losing them if your flight were late. If you were willing to spend your first night in or around Munich, you could pick up advance purchase Europa-Spezial Österreich tickets, online, for as low as €19 per person to St. Margrethen and use the Swiss Pass from there. If you didn't want to use your Swiss Pass that day, you could get a discount fare from the Bahn as low as €39 pP all the way to Luzern.
Lastly, if you wouldn't mind a slightly (~1 hr) longer trip on regional trains, you could buy a €27 Bayern-Ticket in Munich and P-P tickets from Lindau to St. Margrethen (€6,80 pP) either in Munich or in Lindau, and then use you Swiss Pass once you get to St. Margrethen.