Depends what you mean by 'best'...

As indicated above, if you're only there very briefly / only planning to make a very few purchases, then you may be OK paying in euro or by card, and not need any local currency at all. However, if you do want some local currency (which is probably wise if you're there for any length of time), then using an ATM is probably most convenient. Of course, you'll normally pay various bank and foreign exchange fees, so it may not be the 'best' deal, but equally, you can be reasonably sure you're not being entirely ripped off either. There are also lots of forex bureaux around Prague (and presumably in Zurich as well, if you end up there and want CHF). I think last time I needed Czech koruna, I got a better deal at a forex bureau in a provincial town, rather than in Prague - but you may not have that option.

However, someone like AdventureAdam may be better placed to advise than I am.