I was just coming on here to say you can't go wrong in any of these cities. Munich is bigger and has the good and the bad associated with that. All three have amazing outdoors nearby. You would likely love any of the three. And you would equally love Germany's second city (Munich is third in terms of population, GDP, etc.) of Hamburg. Best city in the world ;). Also, for pescatarians, it might have a more accessible food scene. The nearby Wadden Sea is a one of a kind UNESCO site that outdoor buffs love, especially in July.
Strasbourg: Instead of a night or two in Heidelberg, I would recommend Freiburg and the Black Forest for outdoors. Great wine options in and around the Strasbourg region. Walkable city with great places to sit and take it all in over a drink.
Munich: Bigger city, so more options in terms of museums. Lots of good side trips to places like Berchtesgaden or Neuschwanstein or Alpine hiking or nearby cities. I do think based on what you have said that this is the city you would like least of these because it is more of a city. I think you would absolutely love it, but I think you would like the others more. There are squares and such, but the atmosphere isn't as relaxed as Strasbourg or Krakow. Great beer scene (Weihenstephan--world's oldest continuously brewing brewery--is in nearby Freising). Great city for history.
Krakow: In terms of history, this is the best of the three. A lot of it is heavy history, but there is a lot of it. Beautiful square and castle to just sit and have a beer. The old town is a bit smaller. The nearby Park Krajobrazowy Orlich Gniazd is supposed to be great for hiking, but I can't speak from experience.
Your thinking is excellent--not trying to do too much, aware of your interests, and your initial choices are great. That bodes well for a wonderful trip wherever you end up going!