In 1650, the 30 Years War is over and it is once again possible to travel relatively safely through the major trade routes. To travel from Amsterdam to Vienna would probably take about a month, possibly two depending on time of year.

The most probable route, if you are just transporting yourself, and not a large cargo, might be south up the Rhine and it's tributaries to Frankfurt am Main, then southeast overland to Nuremburg (this would be the most difficult part of the journey). You would doubtlessly rest and refit in Nuremburg, then travel southeast to Regensburg, then down the Danube to Vienna.