Munich to Berlin: Train or Fly? & Berlin to Cologne: Train or Fly?

It is about 380 miles from Munich to Berlin. The easiest and cheapest way is by plane uaually. The train trip is about 6 hours and it is perhaps a little more expensive than a budget airline. There is heavy rail in the Munich Airport, but I assume you would take it to the Munich train station to transfer to another northerly train.

Berlin to Cologne is 300 miles and it too might be best traveled by plane. See bahn.de to see what schedules indicates are available.
I have traveled from Cologne south and Bavaria, but I have not been north of Munich toward Berlin.

1) Is there a train station at the Munich airport?

Yes, it is part of the "S-Bahn" (commuter and suburban system). It is the end of the line, two alternative routes into Munich, which will get you anywhere in the centre, or to "München HB" (main station).

2) I know flying to Berlin gets us there much faster, but to take the train would we see beautiful country that we wouldn't see flying? Does this justify the longer trip by train vs flying?

I would question if flying gets you there faster. München to Berlin is 4½ to 5 hours by train, city centre to city centre. That is borderline if you count in getting to and from airports, check-in time etc. And train is less discomfort (One comfy roomy seat). Prices are from €37.90

EXCEPT, Are you doing this on the same day you land, or are you overnighting in Munich first?
If you are doing this the same day, you are already at the airport, so it ways the time balance for flying.
But, make sure you leave enough time after your first flight lands, to allow for the plane being late, or delays in immigration.

3) If we take the train, do we need to make reservations ahead of time or just get tickets after we arrive in Munich?

It is a lot cheaper if you buy tickets in advance (1-3 months). You can do this on the DB website: https://www.bahn.com/en/view/index.shtml

Question) Should we take a train from Berlin to Cologne or fly?

4½ hours by train, by same logic as above, I would take the train.

There are actually a few connections per day that connect the central stations of both cities (Berlin and Munich) in under 4 hours. I have not done the entire distance yet, so cannot comment on the scenery (except that I don't find the scenery in the Northern half particularly noteworthy). If you are already at Munich airport (which is far outside the city, so also far away from the central station), I would probably fly to Tegel (which is fairly close to the city centre of Berlin, if such a thing exists).

If you are flying on Lufthansa, I see they operate non-stops between SFO and MUC, you can get a Rail&Fly ticket. That allows you to take any train to your destination after you land without any reservation. So you don't have to worry about delayed flights. Just take the next available train you want. They just opened a new high-speed section in the Munich-Berlin rail line, so there are some trains that make only a few stops, speeding up the journey.

Berlin to Cologne, I would take the train, but renting a car on arrival may weigh in for flying. Figure this way, it is about 1/2 hour from central Berlin to Tegel, 2 hours from check-in to take-off for luggage check, security, walk to gate, wait to board, board, wait to take off, 1 hour flight, 1 hour after landing to get off, get luggage, walk to car rental, get to the car. 4 1/2 hours.

There is a direct ICE train from Berlin to Cologne every hour and it takes 4 hours and 20 minutes. You can buy advance tickets for as low as 50 EUR per person if you book 3 to 4 months ahead. Now you will need to add about 1/2 hour after arrival for the car rental.

Thank you all for your replies! We are flying into Munich on AA and leaving directly for Berlin as soon after we arrive as possible. Since we are already at the airport sounds like the best solution is to fly to Berlin rather than train, as we would need to take a train from Munich Airport to Central Train Station to catch a train to Berlin. As for train vs flight from Berlin to Cologne, it sounds like we really won't save any significant time by flying; therefore train it is!

I would do the same.
Just a quick remark to Sam: While Tegel has been operating way beyond its design capacity for years, it is still quite an efficient airport. No need to be there 2 hours in advance for a domestic flight. With hand luggage only, you will often need less than 15 (or even 10) minutes from paying the taxi driver to waiting for the departure at the gate, having already passed security. With checked luggage, you will need a bit more time; but I think 90 minutes is plenty (in rush-hour traffic, obviously taking into account some reserve on the way to the airport).