If a ROTC cadet's ultimate goal is to work for a 3 letter agency, is it better to commission active duty or NG/Reserves?

I was a 2ndLt once. I would guardedly take a 2ndLt’s word for career advice. Go talk to people within one of those three-letter agencies for which you’d like to work.

What is important to you, being a military officer or working towards employment with a three letter agency? These things can be done at the same time however each has unique requirements you need to focus on and achieve.

I'll lend my perspective as a former Army Civilian employee and supervisor. My job brought me into contact with many of the three-letter agencies in the Washington DC area, by which I mean NSA, CIA, DIA, DISA, DHS/FEMA, DOT, DOS, and DOJ. The Washington DC metropolitan environment is unique in the US. It's very much a "company town" where almost everybody's job is dependent on the Federal Government in some way. If your goal is to work for one of these agencies, then you should look into their hiring opportunities instead of pursuing a commission. There are many types of internships and fellowships that might allow you to start with an agency soon. These opportunities can lead to entry-level jobs in the GS-12 range with later options to be promoted up to GS-14.

Reserve Component personnel do work for nearly all of the Federal Departments and Agencies. Some civilian jobs are considered Mission Essential and Critical and are closed to Reserve Component personnel; however, there aren't many of this type in any one agency. In most cases, Reserve Component personnel enjoy strong support from their Federal Government employer including military leave with pay to cover your training and active duty time. Of course, you can't be fired or discriminated against because you are a Reserve Component member. There are also quite a few former and retired military members working as civilian employees in the DoD, Services, unified commands, Defense Agencies, intelligence community, Homeland Security, and DOT. Veterans enjoy a preference in hiring that bumps them to the top of a candidate list. If you become a disabled veteran, then you will go to the top of the list (don't spend time trying to become disabled) and it's impossible to hire anybody lower on the list.

If you are committed to a commissioning pathway, I suggest you focus on that first. You might really like the Army and decide the idea of becoming a Government Civilian wasn't that big a deal. Military personnel work in almost every agency I mentioned above, so you could direct your career that way. Select your Branch and MOS with your target agency in mind. For example, if you want to work for DOJ-FBI, go after an Army career in law enforcement and security. If the intelligence community is your target, then become an Army Intel Officer. Or if you want to fly helicopters, get into Army Aviation with the idea of flying for Border Patrol after you get out of the Army. Look on USAJobs web site. Sort jobs by agency and see what the agencies you're interested in are hiring for. Compare those jobs to MOS. Think it through.