Depends on what you wanna do. Salzburg is smaller and arguably more beautiful/romantic, but parts of Vienna are almost as great and it's got much much more to offer. It's pretty diverse too, while Salzburg basically only has some (albeit pretty amazing) Habsburg & Mozart stuff.
Salzburg might be really overcrowded with tourists too, depending on what time of the year you're going there.
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Pappn piefke, er hot noch am ösi gfrogt