The boat trip from Parapat to Samosir Island is 7,000 rupiah one way (2011). You will be asked for the name of your hotel. Most, if not all of the hotels are located right on the lake and have their own place to get on and off of the ferry.
The last boat leaves around 6:00 p.m, so if you arrive too late you will have to stay in Parapat. Fortunately there are also plenty of nice hotels in Parapat.
There are several money changers in Tuk Tuk, but their rates aren’t very good and unless you need to change money for an emergency, it is better to change your money at a bank or money changer in Medan. Better still, go to an ATM - there is one at Parapat as well (bank BNI).