The two cities are very different architecturally: Prague has more Romanesque and Gothic ("medieval") buildings, whereas most of Amsterdam is post-Renaissance (16th century onwards). The latter is also the place to go for modern architecture.

Prague is probably going to be better for hiking, Amsterdam has better museums, as far as beer is concerned it's likely a draw, although it'll cost you less in Prague. Prague might feel more touristy, especially during the time of your trip.

Another thing to consider, AMS is a much larger airport: #3 in the EU and 60M+ pax while PRG is #38 with 1/4 of that number and comparably few long-haul flights, so it'll always be easier to visit Amsterdam during a stopover on any of your future trips. On the other hand, if you're travelling from Brussels this time, Amsterdam is just a 2h train trip away, and no need to take flights at all.

Unless you have a strong preference regarding any of the above, I second WorldLux's advice to go for the one that's more convenient to travel to for you this time.