Constitutionally, Congress is the only branch with the power to remove people from the other branches via impeachment. Congress also has the power to realign the lower courts, which could result in judges losing their courts.
Internally, each chamber of Congress can expel its own members. The Executive branch can remove a President via the 25th amendment, but this intended for incapacitation or deficiency and not an expulsion over political disagreement or criminal activity. I don't think there is an internal method for the Judiciary to expel a member.
-PJ
The department of justice in the executive branch can investigate congress members.
I believe federal judges can be impeached.