There are two major ferry service companies currently operating in Indonesia, PELNI and ASDP.
Just about everything you want to know about them is contained in the following URL with a clickable route map in each of the three layers of Google map.
Click the title portion to find more from related URLs such as WIKIPEDIA Geography and a dictionary in case you find it useful.
Following map is also very useful.
This is a world map, but can focus on any parts of the world and even show up very minor ferry routes.