I don't know exactly how much time you have; are you flying out of Venice on Day 5 or Day 6? And at what time of day do you depart?
I assume you're flying out of Venice because you want to see Venice. So I think you need to spend your last 3 nights in Venice. That will give you two full days there and perhaps a few hours. To keep transportation time to an absolute minimum, I'd choose my other overnight stop from among Verona, Vicenza and Padua--probably either Verona or Padua since Vicenza is smaller and could be a day-trip from one of the other two.
I really wouldn't want to fool with a rental car on this trip. Trains run frequently between Milan and Venice.
Are you flying into Malpensa or Linate?
This is what happens if you try to go to the Cinque Terre and Venice on the same short trip: Taking a train from Milan-Malpensa to Vernazza in the Cinque Terre would take at least 4 hr. 27 min. and could be quite a bit longer if you're unlucky about when you're able to step onto the train. ViaMichelin--thought to be optimistic--estimates a driving time of 3 hr. 33 min. That doesn't include time spent at the rental-car counter, getting lost, or looking for parking. And if you're arriving on an overnight flight, you shouldn't be trying to drive to the Cinque Terre, anyway.
Then 1 or 2 days later you need to head to Venice--another 5+ hours on the train. The trains are fine; it's just that you have so little time, I can't imagine you look forward to spending about 10 hours of your short visit sitting on trains. By comparison, if you select your stops from among the places on the Milan-Venice rail line, you'll have only 2 hr. 25 minutes on trains--gaining essentially a full day of sightseeing time. That's gold on a short trip like this.