well that depends on how you wnat the tsystem to respond.
If you wnat the best boost response and have a systme capable of absorbing a small amount of heat soak, then go with the intake manifold.

If you want it simple and reliable with a minimum of boost spikes go with the compressor outlet.

I like the intake manifold myself. A neat trick for you to try is both. Keep the wastegate set at a constant, and take it for a ride with each. It will tell you how much pressure drop is on your system.
for example you hook it to the intake first, set the gate for 9psi on the guage.
Then you hook the signal to the compressor and see what pressure it makes. If you have say 7 on the guage your intercooler system has 2psi drop. You dig?

That being said NEVER,EVER hook a internal wastegate to a vacuum source. The diaphram is not designed for loads in the other direction and could delaminate/tear.
Again this only applies to internal gated turbos.