Congress, whether by impeachment or otherwise, can remove anyone in the Executive or Judicial branches. Anyone appointed by the President can certainly be impeached and removed.
The legal case of Buckley v. Valeo established the almost limitless power of impeachment. In practice, however, Congress isn’t going to bother much with anyone in the GS system, which has its own system of discipline. It would seem clear that anyone in the 7000 member SES can be impeached.