would we be better off going to vienna for a few days rather than Cinqua Terra because of covid vulnerability. Trip is in mid September
My crystal ball is in for maintenance, but I doubt you would be any more "vulnerable" anywhere in Europe than you would be in your home town.
Well, I think you'll be more vulnerable anywhere in Europe (if not on a hiking trip via rental car) than you are at home, because you'll be out and about so many hours of the day. Opting for hotel rooms that don't include breakfast will help. Breakfast rooms tend to be crowded.
I don't know what the current statistics say for Liguria and Vienna, but both the streets and the trains in the Cinque Terre are likely to be crowded. My main memory of Vienna from a summer visit back in the 1980s is of wide streets and uncrowded sidewalks.
From a purely anecdotal perspective, Italy has a 5% higher vaccination rate (yes I know being vaccinated doesn’t prevent infection but does help reduce illness and viral load) than Austria. Italy also still requires masks on trains etc while Austria doesn’t except in Vienna. You no longer have to quarantine in Austria if you have Covid but you need to wear a mask. Italy still requires isolating.
In terms of meals, you could avoid crowded rooms by having breakfast in your hotel room. We plan to do that in our hotels in Italy when we travel there in October. We also only plan to eat outside when available. We will be using N95 masks inside.