What is the difference between TO-3 and TO-204AA packaging?
Beginning in 1944, an independent standards association called the Joint Electron Tube Engineering Council (JETEC), began standardizing the shape and numbering of vacuum tubes.
When semiconductors rapidly began to supplant vacuum tubes, JETEC was renamed to the Joint Electron Device Engineering Council (JEDEC) in 1958.  They gave things like diodes and transistors of varying packages the familiar numbering we know today.  The original system was fairly simple - packages were simply given new numbers sequentially.
So yes, that means the TO-3 package is the third transistor outline (what 'TO' stands for) to ever be submitted.
This system had flaws however, namely that should any company create a new package that was essentially just an earlier TO package but with some slight variation, they would have to be given an entirely new TO number, making that variant TO-'whatever the next number in the sequence was'.
As you can imagine, having completely unrelated numbers being used to specify what were essentially identical packages, save for some minor (but potentially important for some applications or situations) was confusing and unwieldy.
So in 1968, JEDEC decided to create new system, and all those TO packages created prior to 1968 were given completely new numbers, but now as determined by the new system.
This new system uses the first digit to designate a family of packages that are similar in shape or function.  Anything beginning with 2 is some sort of power transistor package.  Letters were given as suffixes to account for small variations on a specific package.  TO-204AA is simply what the original TO-3 package was renamed to.  Other packages in the '2' family are things like the ubiquitous TO-220, or its surface mount cousin, the TO-263 (D2PAK), and of course even beefier packages like the TO-264.
This happened in 1968 as I mentioned earlier, which means that, at the time I write this, the TO-3 hasn't been called the TO-3 for over 50 years.  It was only called the TO-3 for the first 10 years of its existence, and for the remaining 52 years, it has been the TO-204AA.
But it was so early and influential that to this day, I would say most of us still know it as the venerable TO-3, purveyor of electrons and (probably a lot of) heat.
So, to be clear:
The TO-204 is group of similar packages that are all essentially the TO-3 but with slight variations.
The TO-204AA package matches the original TO-3 case in every respect.  In fact, so much so that it is more of a TO-3 package than a lot of transistors considered to be 'TO-3'.
TO-3 was the older, original designation, but if you've ever opened up old equipment, or just gotten your hands on some older TO-3 power transistors, you'll probably notice they don't quite look like modern TO-3s, and there was a surprising amount of variation between them.  Some had thinner or thicker leads, longer leads, different can heights and more or less founded edges, even thinner or thicker base plate.
A lot of packages had similar problems, and this is a large part of why JEDEC decided to toss out all the original names and start from scratch just 10 years later.
There are other packages in this family which would have originally simply been called TO-3s, even though they are slightly different.  There is the TO-204AE, for example, which is identical to a TO-204AA, save for that the leads are 60 mils in diameter instead of 40.  There are also TO-204ACs, ADs, and even others.  Their will probably be more variants in the future - the TO-3 will never die, though it might get renamed a few more times.