For at least a little while you best bet will be a infrared camera to observe them from a distance. While they may work hard to mimic the characteristics you can see, they may not have tried to mimic thermal emmittance patterns yet. There are several reasons you probably already have one readily available.

Simularly, their density is likely to have changed as silicon has heavier nuclei than carbon.  One could place a scale in thoroughfares or require them to step on it before meeting with you. 

An Xray would likely work if you can convince them to walk in front of a source.  I would not leave one out to give all your crew cancer needlessly.  Us it to screen those entering from outside. The benefit here is you can screen their internal structure.

As I do not know exactly what molecules/polymers/etc they are made out of, however, I cannot predict how these properties would change.  I can only know that they likely would have.

An IR spectrometer would work well if their skin is still made of a silicone matrix or their blood is still artificial. But that would only help when the start finding a way to mimic your blood. As you need a reliable sample which means you need to take it.  The main thing there is to not let any of them know how you are testing them... kill them if the test is positive.  If you could build a portable, long range, broad spectrum spectrometer you would tax their mimicing abilities to their extreme.

Passcodes work well unless they can extract them from your wounded/dead/tortured comrads.