You could try Eurolines and they have bus services from and to all the major European cities. They're connected with National Express, a bus service I've taken many times and don't have any compalints. If you book online you're likely to save a bit of money too. Here's the link:
Renting a car can be expensive depending on your age for insurance so it all depends on your budget. Check out a few of these sites:
As for the train, there is only one train that directly connects Prague and Amsterdam. The train will definitely cost you more than the bus will. This is the site for the Dutch rail: http://www.nshispeed.nl/
Here's a link to a useful German railway site as well that you can try: http://reiseauskunft.bahn.de/bin/query.exe/en?newrequest=yes&protocol=http:&
It might actually be worth it to fly. www.skyscanner.com has some great flights to the Netherlands for about 100 Euro return that you might want to consider if you're short on time.
Hope this helps! about 8 years ago