Ethan works at the Impossible Mission Force (IMF), which in the movie is a US government office that use the services when even the CIA can't interfere in black ops. Why the IMF isn't public like the CIA?
The IMF is a specialized group of expert agents that remain hidden from the public eyes. If the IMF were revealed to exist, the United States would be expelled from the United Nations and banned as a "pariah state".
Ethan and his team work for undercover operations behind CIA's central operation. Ethan is not working at the Clandestine Service because he is operative in the USA and Clandestine Service doesn't work inside US; remember the first movie, but he is also doing work at every corner of the world.
Ethan Hunt would be a Special Agent administratively speaking. Why? In the CIA website you could see:
Special Agent/Investigator – CIA Salary Range: $74,872-$136,771
What are the abilities of the special agents?
(...)responsible for conducting inquiries regarding possible violations of laws, rules and regulations; gross waste of funds; abuse of authority; and danger to the public health and safety within the CIA. Individuals who want to become CIA special agents/investigators must meet the minimum requirements for this profession, which include possessing a bachelor’s degree and at least three years of investigative experience (...) Candidates for CIA agent jobs must have considerable knowledge of criminal and administrative investigative techniques and procedures, and they must be able to assemble large quantities of data and draw appropriate conclusions.
This is considering he is the chief of the team and have more experience than the other members. So now, what would be the salary of the team members? They could be Protective Agents. Again, according to the CIA website:
Protective Agent – CIA Salary Range: $50,408-$95,026
Protective agents, under the Directorate of Support, are responsible for providing support to a number of protective operations, as directed by the Director of the CIA. These CIA agents are often deployed across the globe to perform sensitive operations that support the agency’s protective requirements. They are also often responsible for participating in training and operational assignments.
The team members are earning between USD 70,000 and 95,000 because all of them have extra skills (applied science, special training at some area), which I think are compensated with money.
What I'm not considering is IMF is an undercover office which won't appear in the General Budget as "IMF" but in other sort of offices such as farming research or applied science research, etc.
In conclusion and considering all the jobs made by Ethan since the first movie I think he's earning the top salary for a Special Agent, and according to the information is USD 136,771, without considering the taxes.