Go for the Ministry!

Just to shed a little light on the situation for reference and information!

A civilian officer in any of the strategic organizations (NESCOM and others) is not a GAZETTED Officer. Their service rules are non-statutory as they have not been published in the Official Gazette of Pakistan. You cannot challenge the authority on whatever decision they may make. This has also been clarified via an Ordinance in March 2016 and later on, an Act passed in July 2016 by Parliament. Being non-statutory means 'Mubara E Qanoon' or you can search via google about its legal effects.

Your life will be restricted. No smart phones in the office premises, you have to keep a simple phone. No internet in the office except a designated area where limited number of computers are available, being in SPS-8, you'll earn about 65k (take home salary) but according to my point of view, its not worth it if you have 2 choices.

You will have to face periodic security clearances depending on your security category, you'll have to limit your social life, you will have NO authority, absolutely no authority.

Which facilities, perks and privileges are you talking about? Medical? Pension? Transport?

Being in NESCOM, you'll neither be a Civil Servant nor a Public Servant! NESCOM has no housing scheme (YET, one is going on but is in far flung area). Being an autonomous body, it has very low quota in allotment of plots scheme via Federal Government Employees Housing Foundation (FGEHF).

Now lets analyse the Ministry, a Gazetted Officer with authority. A Civil servant drawing pay from AGPR. House Building Advance (Loan) or Motor Car Advance (Loan) can be acquired after a few years (in NESCOM, the people with more age enjoy this facility, so you have to be at age 55+ to get somewhere in 1st ten, they only grant 5 to 10 people in one financial year). In ministry, Civil Servants Act will apply which is a very well and brief document providing clear cut instructions which you can also take to the court if aggrieved with.

Forget NOC's Sir, even if the bond period crosses, you'll not be easily granted NOC to apply any where, they even curtail staff members' rights in this regard.

FPSC does not grant the age relaxation to CSS aspirants from AUTONOMOUS BODIES and NESCOM is an Autonomous body, you can have the age relaxation in Ministry so you can have more time to prepare

Another thing, you have to be married to have Hiring facility in NESCOM, you cannot have medical treatment for your parents before completing 3 years of service. Parents cannot have a prolong treatment just a casual checkup or diagnosis. But in Ministry, you can hire a house if you are living with your parents (No restriction of marriage), you can have medical facility for your parents.

The above analysis is my own and my own only. I wrote what I see from my perspective.

The decision, I leave to you and your fine sense of judgement.

If you got any question, my email address is at my profile.

Best of Luck Sir!

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ALHUMDULILLAH!
Pakistan Forever <3