Berlin and munich

Because your chosen destinations were both targets of heavy WW II bombing, I'd suggest breaking your 6-7-hour train trip with a stopover (1-2 nights?) in Bamberg, a smaller city with an old-world town center - and a UNESCO World Heritage site - that is on your route.

http://us.hellomagazine.com/imagenes/travel/201204167748/Bamberg-Germany-photo-gallery/0-36-599/a_0137_0007-a.jpg

http://whc.unesco.org/en/list/624

Berlin is a sprawling city without a real central district and well served by public transportation, so the location you choose for lodging doesn't necessarily have to be near "sites". With that being said, avoid the hotels around the Hauptbahnhof. Nothing wrong with the hotels themselves, but the immediate vincinity is kind of a no-man's-land of construction projects.

In Munich, by contrast, you probably want to stay as close to Marienplatz or Odeonplatz as your budget allows. Most of the stuff that tourists come to visit in Munich sit within the relatively compact area inside of the inner ring.

I am quite fond of the Motel One chain and they have several locations in Berlin and in Munich. Have stayed near the train station in Berlin and actually found it made it easy to take trains to other parts of the city, or to go to Potsdam.

"What is suggested airline to fly from/return to USA"

I haven't researched the issue extensively, but offhand, the only airline I know of that flies nonstop from the US to both Berlin and Munich is United, from Newark. If that's convenient for you, that will be easiest. Otherwise, Air Berlin flies nonstop from JFK to Berlin; Lufthansa flies nonstop from JFK and Newark to Munich; United flies nonstop from Dulles to Munich; and American (formerly US Airways) flies nonstop from Philadelphia to Munich. Those are just the airports close to Harrisburg.

Of course, with one plane change, the options are many. For instance, Frankfurt has lots of service from JFK, EWR, and PHL, and you can change there for frequent domestic flights to Berlin or Munich.

If you want to use Harrisburg airport, you can fly back from Munich to Toronto to Harrisburg, as well as connecting in the US (multiple US airports get nonstops from Munich). But to get to Berlin from MDT, options seem more limited (very few nonstops from the US to Berlin, so you'll probably end up making a few changes).

Note that Air Berlin is a budget airline; the biggest manifestation of this in the trans-Atlantic service is that they charge you to select seats in advance. They do feed you, and they don't charge for the first checked bag (at least on JFK to TXL). And they also offer Economy Plus.

To find all your options, look at Kayak, Matrix ITA, Google Flights, etc. When searching (assuming you have flexibility), be sure to check "include nearby airports." Using the code BER will bring up both of Berlin's airports.

I always consider the best airline to be the one that gets me where I am going, on the schedule that works, and the cheaper the better...and if the ticket is cheap enough, I will reconsider where I am going and my schedule. Using the search sites (Kayak, CheapoAir, etc) is a good start, if a major airline comes up and I can get the same deal through them, I book with the airline.

For rooms in Berlin, look for areas that interest you, then I had good luck with comparing Tripadvisor, Lonely Planet, and Ricksteves guides. Same strategy for Munich.

Public transport works great for your plan, I second the idea of maybe making a stop someplace smaller and older as a change of pace or you could also plan some day trips outside of Munich (the castles near Fussen, Salzburg, etc)

Delta partners fly into Berlin, I've done that route twice. I think the airline was KLM.

I also recommend Bamberg on the way to Munich.