Can you help us decide?

You would neither need a car in Munich nor in Vienna, as both cities have an excellent system of public transport.
But if I had to choose, I'd vote for Vienna, which in my view has more to offer than Munich.

I've been to both twice and love them both, but if pressed I might have to agree with the other poster and recommend Vienna. Both had good walking tours on offer and both have nice old city centers, but I'd probably give the edge to Vienna on museums and palaces and maybe even churches. The weather in March is likely to be much the same in both - cool, good chance of rain, snow less likely as average daily highs would be around 50 degrees F.

I vote for Vienna. Actually Budapest, but .... although there are tons of nonstop from Frankfurt and several Legacy and Discount airlines nonstop to Atgens every day but Tuesday and Thursday (which I guess messed up that idea unless you go on to Athens on Wednesday)

Thank you all. We’ve been to Budapest too. So far, Vienna sounds like the preferred choice.

If you are an art lover - I would pick Vienna. We went to Munich and Vienna on the same 2015 trip. Both cities have excellent food and beverages, but overall I would take Vienna for the art.

Vienna would offer some outstanding indoor venues, museums. You will need to pack for different climates for the cruise.
Where does your cruise go from Athens?

The reason people go to Munich is to visit Bavaria that you need a car for. Munich itself is not a must-see in my opinion compared to Vienna. While in Vienna, take a day trip to Bratislava’s old town by direct train (1h).

Another vote for Vienna. The weather won't be magnificent but the art and music will. Put in your order for some sunshine for your photos since you will be battling the gray skies. However, the Heurigen will dissolve the gray and brighten your days.

Then I say Vienna .... or Istanbul

Yes, I thought about Istanbul too. But flight from Frankfurt is longer and not at a good time.
Our cruise starts in Athens and goes to several ports in Greece before going to Croatia and ending in Venice:
Athens (Piraeus), Greece
Santorini (Thira), Greece
Katakolon (Olympia), Greece
Corfu (Kerkyra), Greece
Kotor, Montenegro
Dubrovnik, Croatia
Zadar, Croatia
Koper, Slovenia
Disembark In Venice

Sounds like a fantastic trip

I've been in Vienna early March and the weather varied a lot: one day looked like early spring, and the next day winter returned, with wind, grey skies, and sprinkles. I didn't find the weather a hindrance. However, what I really missed were the gardens in bloom. There were no leaves on the trees and nothing in bloom.
But Vienna is a fantastic city , so I vote for a visit to this city on your trip.
Safe travels!

Another vote for Vienna for the variety of wonderful museums, St. Stephan's Cathedral, etc. During our last stay, we stayed at a very nice hotel, Hotel Am Stephansplatz, across from the cathedral. There's a handy metro escalator right there.

Thank you everyone again for your advice and suggestions.
Vienna seems to be the answer.