Hello from Prague where I am just finishing up my 3 night pre-cruise extension with Gate 1 cruises. AMA waterways extension stayed in our same hotel and had virtually the same itinerary.
I arrived in Prague a day early for the tour and simply reserved a room at the same hotel (Hotel Cosmopolitan) independently since this saved me $100 over going through the cruise company. The hotel allowed me to stay in the same room for the entire stay. The hotel is lovely, well located and good breakfast buffet.
I used Prague Transfers for my ride in from the airport. Cost for private driver meeting me at arrivals was $35 cash. The true bargain hunter over 65 can take the bus for free into town, but I like to treat myself sometimes.
What I did as part of cruise extension package: Walking tour of Prague Castle grounds, Jewish Quarter and Old City Square, Bus trip to Terezin the Nazi deportation ghetto and gestapo prison (hard to see but we must always remember), walking tour of the Lesser City and the Charles Bridge. The tour manager and cruise director also maintained a welcome desk where they could advise people on their independent plans.
What I did independently:
WWII walking tour with Living Prague Tours. (Amazing! Excellent quality guide. I can recommend.)
Climbed the old clock tower at City Hall, visited the Klemetinum Library, attended a classical music concert at the Mirror Chapel, walked around many areas of Prague.
We head tomorrow morning for Pilsen and then onto Regensburg to join our ship, The Monarch Queen in the afternoon. The cruise director has announced that the entire river stretch to Budapest should have sufficient water levels.