One year we stayed at Hotel Julian for 3 days--loved it. Book with them directly if you want a better price. Rooftop terrace with good views of the city and an excellent breakfast.
It is quiet (we slept with the windows open!!) as it's away from Old Town and Prague Castle, but a tram stop is only a 5 minute walk away. Public transit in Prague is great. For your time frame I would suggest a 3-day pass for each of you. It's around $15. Save your feet and save yourself the hassle of individual tickets. We used the map in the Rick Steves book extensively during our month there last May getting around on transit, to the point of using tape to keep it together.
For hotel Julian, from the train station you would take tram 9 to Svandovo Divaldo. The hotel is just around the corner.