Take a regional train from Deggendorf to Plattling (9 min), change in Plattling to another regional train (about 1½ hr) to Munich. The change in Plattling is an 8 min, one platform change, which should not be a problem unless you are weighed down by luggage from your cruise. The trip should take less than 2 hours.
A Bayern-Ticket for 2, for 31 euro, will cover the entire trip as well as any local transportation once you get to Munich.
I would stay in Munich near the town center, Marienplatz. Here is a pension just a few blocks from Marienplatz. Alternatively, you could stop in Freising on the way to Munich and check into a hotel there. Then continue on to Munich, spend time sightseeing and return to Freising for the night, all on the Bayern-Ticket. The next morning, it's a 20 minute, 2,80€/person bus ride from the Freising Bhf to the airport. Here is a place to stay in Freising.