I think you're about spot on with 5 nights. A few more days wouldn't hurt, but you can do the city justice in 5 days. Lots to see and do, most in the inner city, so good that you've situated here. That way you can do as much or little as you like. Most of what there is to see here relates to the Hapsburg dynasty, and some activities require advanced ticket purchases (eg. Opera, famous Lipzinger stallions, Vienna boy's choir, etc).
As far as cruises go, I'd really recommend the cruise down to Bratislava. About an hour downriver, an hour and half upriver. And very beautiful cruise. Bratislava is a fun and historic place and works well as a day trip destination.
Now for what will seem like shameless self-promotion, but there's a lot of information on what to see and do on our website. There's a 2 part series on Vienna I posted on this website in the wee early years of TravelGumbo. Part 1 and Part 2 can be reached by clicking their links. The Bratislava post can be found here.
Buon viaggio 2U2!