I´m pretty sure a taxi driver will be happy to drive you to Vilshofen but it might be a bit pricey
As for public transportation:
Bus 635 from the airport to Freising train station (2.40 Euro single ticket)
regional train from Freising station to Vilshofen station (Bayern ticket is 29 Euros for both of you, don´t know the single ticket price)
The train runs app. every hour with the bus leaving at 15 min past the hour from Terminal 2. Whole ride is about 2:10 h.
The train station in Vilshofen is withing walking distance to the Danube river.
Check on www.bahn.de