SystemClock.sleep() vs. Thread.sleep() while waiting for a semaphore loop

First of all, do you really need a wait loop? You can typically solve your problems using proper notifications, i.e. having an Object, calling wait() and notify() on it or other means (like a blocking queue, or Semaphore.acquire() in your case).

That said, if you really want a polling loop (which you really shouldn't do unless you have to), I'd stick with Thread.sleep(). There's not much of a difference, as the documentation says, except that you have the option to interrupt a Thread.sleep(). Don't rid yourself the option to do so.

Note that in case of Thread.sleep(), you're going to have to catch that exception - if you're extremely lazy, you'll probably stick with SystemClock.sleep().