We booked two tours through private-prague-guide.com The first was an architectural tour and we saw the amazing diversity of architecture throughout the city. Our guide was wonderful and the 5 hours flew by (well, mostly, it was the hottest recorded day in Prague history!). I believe the cost was 96 Euro for 3 of us plus a few extra czk for tram tickets, water, snacks, and tip. Definitely worth it-we were on both sides of the river, and it was not just an architectural tour but historical and cultural tour as well. I'd say the only overlap might be at the Castle complex but I'm sure you could either opt out of that and spend more time in another area. It was really thorough!
The second was a tour of the Jewish Quarter which was also good, although the tour guide was separate from Museum(s) admission so that took a little thought-did we want all 4 synagogues or not? Which ticket? Our guide was helpful and since this was our second (very hot) day of touring led us to Maisel, Pinkas (which has the walls with the names of the victims of the Bohemian Shoah and drawings from the children of Terezin Ghetto) and Jewish Cemetery. The Pinkas was quite emotional! We skipped the Klausen and the Spanish synagogues. There's a good website that describes what sites have what (they're all like museums with different and complementary displays)- jewishmuseum.cz .
Hope this helps-even if you didn't have a tour guide for the Jewish Quarter, it's helpful to know the lay of the land, which apparently I forgot to research before I went. Prague has so many fascinating areas of interest you could spend a week there discovering, easily.