Originally Posted by
JBord
Go with Amsterdam then. Better museums but, in my opinion, beer is not as good as Prague

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Well the OP is already visiting Belgium so (s)he can definitely enjoy some great beers when (s)he's there!
Make sure to visit Delirium cafe in Brussels, they have a HUGE assortment of beer (Guiness World Record holder), my usual tactic of choosing a beer is taking the menu and blindly pinpoint something, otherwise it takes you ages to decide!
For transport between Brussels and Amsterdam I would personally choose the train over flying or renting a car. The problems with flying are obvious, you lose a lot of time on the airport and getting to/from it. The problem with renting a car is that it's probably more expensive (unless you travel in a group) and you have the hassle of finding+paying for parking space, etc... Public transport is pretty decent in both the Netherlands and Belgium.
Cheers!