Here are a few more places that are within 5 mins walk from each other, just take the green line metro to "Jiřího z Poděbrad" and great beers are close
https://www.facebook.com/beergeek.cz - They have a bottle shop and a brand new bar. They have the more expensive beers, maybe 50/50 split on Czech and imported. They take great care of the beers and have beer sommeliers on hand to describe the beers if needed.
http://www.obycejnysvet.com - A classic Czech pub that has a great selection of Czech beers from medium sized breweries. Not craft beer but not well known beer either.
https://www.facebook.com/pivoaparek - Again lots of beers from small breweries and a good selection of bottles. Name means "Beer and Hotdog", that should say it all
And if you fancy a curry after all that beer then one of the best Indian restaurants is right next to these places too:
http://www.pind.cz
Lastly, right on Wenceslas Square is this place:
http://www.vytopna.cz/praha/
They have a good unfiltered lager but the attraction is the delivery method. The whole place is rigged up with a model railway and your beer is delivered directly onto your table on the back of a model train. Kids love it, big kids like me love it more