I second In De Wildeman. Awesome little beer place.
't Arendsnest is also awesome. They serve only Dutch beer and have a ton of gems, lots of little indy producers. Try some Bokbier (not the same as German Bock). You should be friendly with the bar staff and ask for recommendations. If you try stuff randomly, you're going to drink some crappy beer also. I tried a few random, had no luck, then trusted them and they steered me well.
There are also a couple of brewpubs. The one with better beer, IMHO, is Brouwerij 't IJ. They're not right in the center, more over by the maritime museum. Look on a map. And they have severely limited hours, so be aware. From what I remember, open from 4 to 8PM or something ridiculous.
Maximiliaan is the other one that I went to. Beer wasn't as good but they had some good food.
Another decent place is Belgique:
Anyway, last time I was there was in 2000. So, my word is old on these places. But there are lots of great beer places there. Just be aware, if you smoke, the good beer places don't allow it and the smoking places have crap beer. When I was there, I alternated between the two. If you want a smoking place, check out Greenhouse. They have a few places and they actually put some work into designing the space so it's cool and interesting rather than the usual crappy places.