This is the reason I love Quora: questions like this. And the person who asked you to post this question, he wouldn’t happen to have the last name “Blofeld,” does he?
At any rate, you have to look at three factors: the type of super villainy you are up to, the support network you have, and the details of your evil plan. If you are up to super-destructive villiany then you need to look into a location that is either A) mobile (like an oil tanker or a submarine) or B) far away from the target area (like a space station). If your villainy is rather low scale and/or lame (like drug trafficking or stealing water) then you want a compound close to infrastructure that supports it (highways, pipelines, airports, etc.)
If you are a super-villain with a huge support network (like SMERSH or SPECTRE) then the sky is the limit (see aforementioned “space station.”)
Finally the details of your plan is important. If it involves controlling the world’s media, then you can hide in plain sight (like, you know, Rupert Murdoch). If it involves controlling mankind’s hearts and minds with electronic devices, then you probably want to be situated near Silicon Valley (like, you know, Steve Jobs). And if you want to launch space ships into orbit then the Amazon or a hollowed out volcano may be your thing (like, you know, Richard Branson).
Just remember, those who fail to plan super-villainy, plan to fail. And when you see James Bond for the first time, do the smart thing: SHOOT HIM.