score:3
You should be able to use mapy.cz. It supports bike navigation in the whole of Czechia, including Prague. It also has apps for Android, iOS and Windows Phone.
Unfortunately, the website seems to be Czech language-only. At least the Android app is (mostly) translated to English, though.
The Android app also supports downloading the map, which can be useful for example if you have access to a wi-fi, but don't have a data plan.
Upvote:4
Na kole Prahou (iOS/Android) is a bicycle navigation app from the city of Prague that is specifically designed for that purpose: finding the most bike friendly or fastest route (with or without bike sharing integration), filtering on traffic or elevation profile.