It's hidden, but if you go under Pre Tour on tour page's website, you'll see this:
Here are suggestions for sightseeing in Prague that we will not be doing as a group (see the guidebook for details): the museums of Prague's Jewish Quarter, Museum of Medieval Art, Mucha Museum, Municipal House, Havelská Market, National Museum, Toy and Barbie Museum, boating on the Vltava River.
Of those, I highly recommend the Municipal House if you have any interest in Art Nouveau; note that you need to pay to take a tour, as the best parts aren't visible for free. For me the Jewish Quarter was a bit of a let-down as it was so hyped, but it's still worthwhile. Note that it takes several hours to see even at a rapid pace, and if you take your time, you could spend much of day there. I really liked the Jubilee Synagogue (Jubilejní Synagogue) with its mixture of Moorish and Art Nouveau styles; it's not in the Jewish Quarter, but is included with your ticket to the Old-New Synagogue which is in the Jewish Quarter. The Mucha Museum is very good, and is small so it doesn't take long to see.
I agree with the suggestion to go to the Charles Bridge as early as possible before the crowds - you can see what it's supposed to look like when all the vendors and crowds aren't there. I also agree that with all its eye candy, just walking around Prague is a great thing to do.