Austria/Germany for 5 nights for family of 4 traveling with teen boys- Summer '17

I'm not one of the board's experts on Bavaria, so I'll leave it to someone else to suggest a place or two to stay on the way and possible great deals on rail tickets. I do want to warn you that it is usually extremely costly to pick up and drop off a rental car in different countries. Of course, you could take the train from Zurich to a convenient German city and get a car there. Or you might be fortunate and find a great rental rate with a smaller than usual drop charge.

There are several beautiful historic cities up near Warnemünde, including Lübeck and Schwerin. Schwerin has a lovely palace on a tiny island in a lake, surrounded by pretty gardens.

You'll be getting your mountain fix at the beginning of your trip, and where you do that will affect what other stop(s) are practical on the way north, so I'll just mention one possibility:

One of my personal favorites in eastern Germany is the truly stunning town of Quedlinburg. The cathedral has an extremely impressive treasury with a WW II-era link to the US (Google for details) that might interest your sons. It has a castle, too. You can rent a good English audio guide from the tourist office, and I think there may also be English-language tours.

Dachau is easily visited from Munich, or you could go to Buchenwald, which is outside Weimar. It was used after the war to house people who ran afoul of the new communist regime, so it has two layers of history to explore. Weimar is an attractive city itself, and the lively university city of Erfurt (not blasted to nothing in the war) is full of half-timbered architecture. Those two cities are fairly near Quedlinburg.

One of my personal favorites in eastern Germany is the truly stunning town of Quedlinburg. Mine too. It's a great jump-off to explore the Harz mountain region as well (although you will have seen the far more impressive Alps at the begining of the trip). Quedlinburg is also fairly close to a one of Germany's better preserved medieval castles, although the name escapes me at the moment.

Coming from Zurich, a good place to sample the Bavarian Alps is Oberstdorf. You can ride a lift to near the summit of two different mountains in the vicinity. The town itself is also very nice.

There are inexpensive international train fares purchased in advance for specific train journeys. In the situation you describe I might travel from Zurich to Munich on day 1 and stay 2 nights in Munich. Your family with teenagers could visit Dachau and either the Deutsches Museum-- great science museum or the BMW museum.

After Munich you could rent a car and head up to the Harz Mountain/Quedlinberg/Wernigeroda or other eastern Germany area for 2 nights on your way up to Warnemunde.

"...castle, Bavarian alps, history - concentration camp....looking for something unique to see in Austria and Germany."

Neuschwanstein "castle" in the Bavarian alps town of Füssen is unique, but not a good idea if by unique you mean having an unusual experience, as that's what every visitor to Germany seems to have in mind. And it's not even a castle but a late 19th century palace.

And since you've seen Swiss alps that dwarf all other alps, I'm going to suggest you take a different route altogether.

Zurich makes it simple to get into Germany. You can be in Stuttgart in under 3 hours by direct train. The Porsche and Mercedes-Benz museums there are unique - and a big draw for many. Or you could reach the attractive Black Forest town of Villingen in about 2 hours. It's an old-world hidden gem that is unique in the sense that very few North Americans (including Rick Steves AFAIK) have set foot there. From Villingen or one of the other nearby towns you could ride the scenic Black Forest Railway to other BF villages and to the Vogtsbauernhof open-air museum in Gutach (near Hausach) where you can take in local history and culture over the last few hundred years. Next door is a summer bobsled run.

Map, BF Railway

Gutach

Gengenbach

Castles: Heading north from Stuttgart and the Black Forest, there's no better place than the Middle Rhine Valley, a UNESCO World Heritage site full of old-world towns with half-timbered buildings and 40 castles in 40 miles of river valley. Bacharach and other villages - Oberwesel and Braubach for starters, are charming and worth visiting - Braubach especially for Marksburg Castle.

Concentration camp: IMHO this is a good way to make oneself and one's children pretty miserable for about 24 hours, a lot to ask of oneself with just 5 days in a country. If you have an interest in WW II, the Remagen Bridge Museum in Remagen on the Rhine would be a good place to stop. Another option is the Nazi Documentation center in Cologne, housed in a former Gestapo prison. But indeed such a place, while informative and interesting, may reinforce media stereotypes that Americans carry around with them about Germany.

We recently took the train from Zurich to Innsbruck, and then from there to Munich. We loved Innsbruck; we found it an easy city to navigate on foot, and it is fast and simple to get up in the mountains for beautiful hiking and eating at the mountain "huts." The train to Munich was just over 2 hours. From there it is very easy to get to Dachau by public transit. We found the exhibits at Dachau eye-opening even though we had extensive knowledge about the holocaust prior to arriving.

You are very fortunate to be taking your family on a cruise around Scandinavia. We took a cruise out of Copenhagen a year ago and it's a vacation of a lifetime. St. Petersburg was downright overwhelming the two days we were in town with a tourguide.
Unfortunately flying into Zurich is not the most efficient way to get to Warnemunde. And it's a very long way from Zurich to the northern German coast.
I would suggest you do as previously mentioned and take a train from Zurich into Munich. You could rent a car and go south into the Austrian mountains--a 2 hour trip. And the city of Munich easily has enough to do to keep your family busy for four days. Or you could take a day trip over to Salzburg.
Have you considered skipping the long train trip and flying from Munich to Hamburg on Air Berlin, a budget European air carrier? It'll give you more time in the very satisfying Bavaria.

Have you considered skipping the long train trip and flying from Munich to Hamburg on Air Berlin, a budget European air carrier? It'll give you more time in the very satisfying Bavaria.

In fact, adding up citiy to city travel time, flying will save you barely 1:30h. But some times it is even cheaper than a discounted rail ticket, so you should compare.

If the boys have an interest in aviation, see Flugwerft Schleißheim, a 20-minute S-Bahn ride from the Munich Hauptbahnhof. It is the aviation branch of the Deutsches Museum, and located on a WW1-era airfield north of town. During the present renovation project at the main Deutsches Museum campus downtown, most of the aircraft normally displayed there have been relocated to Flugwerft, as well. There is also Verkehrszentrum, the Deutsches Museum branch featuring all manner of surface transportation.

As an alternative to Dachau, consider a visit to the new NS Doku-Zentrum, on Briennerstraße, on the site of the Third-Reich-era Nazi party headquarters. Next door is Hitler's office building (where the 1938 Munich Accord was signed), now repurposed as a high school for music and theater. The city's website offers free downloadable maps and audioguides of thematic walks tracing the history of National Socialism in Munich.