Munich is south of the airport, Nürnberg is north. Going via Freising shaves some 60km off your journey, but has the disadvantage of a slower and less frequent (but a tad cheaper) train service. The bus to Freising is 3ph, so you'll get there quite easily. When you know your arrival time at MUC, check the website if there's a train via Regensburg (direct or ALX,RE) going at the right time. If there isn't, take a faster train from Munich.