Of course they were and are part of the Executive Branch. But the precedent for many decades was they were independent. Because not everything that happens in this world is governed by an explicit law.
And what is happening is unprecedented and right to be concerned about it.
However, we are several years into a trend of courts curtailing the ability of agencies to write laws themselves without explicit and detailed direction.
West Virginia v. Environmental Protection Agency is a good example of this. Congress didn't vote on the EPA regulating CO2.
And what is happening is unprecedented and right to be concerned about it.