Which of these would be a good way to end a campaign?

Scenario 1: Atropus, The World Born Dead finally comes to Toril and it's up to the level 20 heroes to defeat the Elder Evil before it destroys all life on Toril.

Scenario 2: Death Heart, the city ruled by undead comes out of the Negative Energy Plane to wreak havoc and it's up to the party of seasoned adventurers to fight off the invasion.

The ending of a campaign should feel like something that organically grew out of the campaign itself.  A capstone of all the effort that it took to go there.  Thus, if you are already in a campaign, the right answer is the one that feels organic for what you have already done thus far.  If you are not, then the right answer is whichever you would prefer building and running an entire campaign around. 

Those are not things we can decide - if you are in the former situation, we do not have enough information; if you are in the latter then we cannot tell you what you would find more fun to build your campaign around. 

That said, functionally these are nearly exactly the same - both are large threats that spawn lots of undead with their arrival.  Mechanically you’ll have lots of undead followed by a boss dominating your capstone sessions.  So, really comes down to a vibe check between these two options of what you want to do.

I realize we don’t have much context here, but those both sound like they’re kind of dropped in out of nowhere. Is this for an ongoing campaign or are you in the planning stages?

As caerwyn said, if it’s ongoing, then I’d say use whichever one makes sense considering what been happening in the world.

If you’re in the planning stages, I’d say you’re looking much, much too far ahead. Most campaigns either peter out well before 20, or the characters are able to reach a natural, satisfying conclusion well before 20. I know lots of people have the 1-20 idea in their head, but in practice, it very rarely works. If nothing else, it usually takes too long, irl, to get to 20.

I’d suggest something much more vague, the cultists are summoning the horrors of whichever sort. Then when things are wrapping up, you find an appropriate enemy for the ending.