in temps between two bodies is higher. Basically, cold water has more of an effect on hot air than it does on warm air. In this sense, it would be best injected into the metal pipe coming from the compressor as that's the hottest part of the charged system. Intercooling is going to add a twist into that theory though because the thermal transfer through the IC also works in much the same way as the water does. The hotter the charge, the more the IC cools it. The question comes down to which performs better? The IC or the water? I would tend to think that the water has a significantly higher effect than the IC does (per mass of air) so this supports the idea of injecting the water just after the compressor.
The true test would be to have a car with nozzles in both locations and an array of temperature sensors to monitor the effectiveness of both theories. Gotta love the scientific method. =) I hypothesize that putting it just after the turbo will have better influence. Only other problem I can think of is perhaps if the water cools that charge down 'too much' and then it goes through the IC. The test would be to find out if in any realistic environmental condition could exist that the water recondenses in the intercooler. That wouldn't be a good thing.