I'm not familiar with the micro space station but it sounds like a secret location and difficult to get to, which is good. I think the Mighty Avengers headquarters was accessed by Pym technology, right? Thus also a secret location and difficult to get to, which is good. So I vote for those two.

Any headquarters that's right out in the open is ridiculous. Place it in the midst of civilians and it's doubly ridiculous. I know the Silver Age HQs were right out in the open and in the midst of civilians but that doesn't mean it made sense. The Justice League had the right idea with their orbital space station HQ.