From The Airport
The cheapest way will be to take the 119 bus (32kc per person-1 hour ticket) and then the metro from dejvicka to Mustek metro stop. According to google maps it is a 5 minute walk from there, but it can be faster if you walk quickly or slower if you are trying to orient yourself. You can also take the AE shuttle bus (60kc) to the Mian Train Station (Hlavni Nadrazni) and this is also a 7 minute walk according to google maps or take the tram to Vaclavske Namesti (#9 tram). A private taxi from the official taxi pickup is about 600kc, but if you go to my website and look at the Taxi Service page you can call the super cheap taxi and they will pick you up at terminal car drop-off area within 5 minutes of the call and it will cost about 350kc.
From The Train Station (Hlavni Nadrazni)
You can walk about 7-10 minutes or take the #9 tram to Vaclavske Namesti and then walk a few minutes.
From The Bus Station
Walk to the Florenc tram which is almost in eyes sight and a few minutes away from the bus station. Take the tram towards the center and go to Vaclavske Namesti (#3 and 14 tram). From there walk down up Vaclavske Namesti towards the Museum and it's about 5 minutes maximum. Or take the metro line C (red) and go one stop to Muzeum stop and then walk 3 minutes.