Before we move on to other places, I want to show you a third prime photo spot in Prague, Petrin Hill. It's located on the Vltava River's western side, making it an excellent location for photographing sunrise.
But even at sunset, you can get some lovely photos, as seen in this image. I took it during an afternoon in spring with dark clouds above the city. The sun was peeking above the top of Petrin Hill behind me, bathing Prague's spires in golden light.
While you can get to the top of Petrin Hill, even using a historic tram, the best views are half the way up. Walking up this path, you'll find several views just above the Prague Skyline. This perspective creates a beautiful stack of buildings and towers leading to the Gothic church in the background. I still aim to capture this scene on a misty morning with the sun behind the skyline. So I have to return this year.
For the planning of such shots, you can use Photopills or PlanIt.