We have been to both ports several times. We never do ships tours and especially not in these two ports. The train in Zeebrugge is the easiest thing to do, takes about 20 minutes to get to Bruges. When you get to Bruge grab a taxi to the town center. There you can take a canal cruise, a horse drawn carriage tour or just walk. It is beautiful and magical there. You can buy Belguim chocolate. Belgium lace, etc. There are gorgeous churches to visit. If you've been to Bruges before I highly recommend going to Ghent. There is a magnificent, medieval, castle there to explore.
Taking the train to Amsterdam is very easy. I would arrange a tour that picks you up from the train station when you arrive. If you are going to be there when the tulips are blooming they are worth seeing. Also you can see the windmills. There are many wonderful museums and Anne Frank's house in Amsterdam.