FWIW, I’ve known some of the OG NGA people a long time and they always referred to it as NGA in my experience. If anyone referred to it as NGIA I never heard it.

NGA is of course its correct name but if you Google:

" "NGIA" intelligence mapping"

It'll turn up a ton of results where people external call it NGIA including a number of .edu sources...

In some ways I guess it's a bit of a stylistic choice, putting a letter for each of the four words of its name, much as how BBC News does not always capitalize all acronyms. Copy and pasting from their style guide:

"acronyms

Use the abbreviated form of a title without explanation only if there is no chance of any misunderstanding (eg UN, Nato, IRA, BBC). Otherwise, spell it out in full at first reference, or introduce a label (eg the public sector union Unite).

Where you would normally pronounce the abbreviation as a string of letters - an initialism - use all capitals with no full stops or spaces (eg FA, UNHCR). However, our style is to use lower case with an initial cap for acronyms where you would normally pronounce the set of letters as a word (eg Maga, Sars, Aids, Nasa, Opec, Apec).

There are a few exceptions:

    The National Institute for Health and Care Excellence is capped up ie NICE
    Special educational needs and disabilities becomes SEND
    The UK Independence Party is capped up ie UKIP
    Strategic Health Authority becomes SHA ("Sha" looks like a typo)
    Seasonal Affective Disorder becomes SAD ("Sad" would be confusing)
    Where a capped-down acronym risks being misunderstood as a word. 

When abbreviating a phrase, rather than a name or title, use lower case (ie lbw, mph)."