Since you are up for a short stay you need to be close to the must-sees. So i`d say Old town but it won`t come cheap. You could stay a little outside the old town to equally good hotels but cheaper.
We are staying in the Old Town. Location,Location,Location!
For only 3 days, if you can get a good rate, stay in the Old Town, but because the public transportation is really good, it really doesn't matter too much...Just pick a hotel you like & read reviews... Late May towards June is a good time for sightseeing... Have a great time!
The Old town has two parts (to put it simply) the Old Town Square side of the river (Vltava) and the other side of the river the Lesser Town (Mala strana) either of the two are central. The New Town is slightly further away from the tourist locations and not so quiant - so I would look for hotels in Prague 1 (new town again put simply is Prague 2)
Old Town - Stare Mestro for sure
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