I think you're not getting many replies as its generally very easy to do this on your own. For Bruges, the train is quite quick and there is an easy bus to city centre that you catch right outside the train station. Once you're in the main square, you can easily see the main sites. You can decide if you want a canal tour, to climb the tower or to tour the museum or enjoy some chocolate or beer.
I think that you would need to look into one of the fast trains if you wanted to do something similar for Amsterdam. You would have less time, but you certainly could do a boat tour and then a quick visit to the Anne Frank House or one of the wonderful art galleries. The canal boat tours start right outside the main train station.
Maybe this will bump it up and you'll get more answers. You might also post in the transportation forum and ask about the trains to Amsterdam. Also, someone may know of Amsterdam based city tours if you posted that question on the Netherlands forum.