Bearing in mind Alan and Katrina's excellent points - I would sail into Budapest - just a personal preference but I hope to sail the Vienna to Budapest stretch one day. I love the stretch of the Danube at Budapest.
As you would be sailing North-South, Budapest would be warmer.
If you have the time, budget etc there is a lot to recommend a pre/post stay in both cities depending upon your interests.
If there is anything else I can help with, please ask.