You are correct that a nitro group is a deactivating agent. If you draw out the resonance structures, you will see that the nitro group deactivates (i.e. draws electron density away from) the ortho- and para- positions more than the meta-positions. Therefore, a nitro group would stabilize a negative charge at the ortho- or para- positions more than it would stabilize a negative charge at the meta- position. Therefore, 4-nitrophenol (i.e. para-nitrophenol) is more acidic because the acidic OH group is para to the nitro group, whereas the nitro is meta to the nitro group in 3-nitrophenol (i.e. meta-nitrophenol)