There are kosher apartments in Prague Jewish quarter, with kosher breakfasts available. The apartments are just few minutes walk to Synagogue and kosher restaurants. You can see details at Prague Jewish guide (http://www.chabadprague.cz/).
There are also several non-kosher hotels in Prague Jewish quarter within walking distance to synagogue and kosher restaurants, where you can get kosher breakfast upon request. For further details see Prague Jewish guide.
Bellagio Hotel
U milosyrdnych 2, tel. +420 221 778 900, (http://www.bellagiohotel.cz). an elegant italian-style 4 star hotel. all the rooms are equipped with ensuite bathroom, hairdryer, bidet, lcd tv screen, free wi fi connection, safe, minibar, and direct dial phone. the hotel was completely rebuilt from on original residential building during 2002 / 2003.