In my novella trilogy that I am writing, Of Aliens and Men, the leader of the main antagonist faction, an alien organization called the Empyre (pronounced: Em-peer) Empire, Empress Erika II holds nigh-limitless political and military power. I am concerned that she may come off as a Mary Sue-esque character.
Is a character with high political, instead of physical, magical, etc. power, a Mary Sue?
An extremely powerful character (be that magical, physical, political or any other kind of power) is not automatically a Mary Sue. A Sue is generally characterized as being infeasibly competent, and usually takes the form of a wish-fulfillment insertion, either of the author (e.g. Wesley Crusher is often seen as this for Gene Roddenberry in early Star Trek: The Next Generation) or for the reader.
Because of this it's rare for antagonists to fall into being a Sue (sometimes referred to as a Villain Sue) but it does happen - if you've ever had the misfortune to read a terrible fanfic where the heroes of the canon find themselves being soundly beaten by a new-for-the-fanfic villain who seemingly has an answer for anything and everything 4 weeks before they even think of trying it, even though it makes no sense whatsoever you probably know what I'm talking about.
So an evil tyrant who rules vast and powerful Evil Empire(TM) isn't necessarily going to be a Sue - and indeed there's no particular reason to assume that they are.
If they are going to beat the protagonist (be it temporarily or permanently) you just have to make sure that it makes sense for the character, e.g. if they can show up with overwhelming military force and crush the good guys in a battle that's what we expect the leader of a large empire to be able to do.
Frame challenge time...
So I don't actually think "is this character a Mary Sue" is a particularly useful question to ask yourself as a writer, because it makes you look at your story in the wrong way. You start thinking of traits like power, skill, beauty, etc. as problematic in and of themselves - but what you really need to look at is what role they're playing in the story.
Case in point, your question. Having a hugely powerful antagonist can be a very good thing for your story! It allows you to challenge the heroes in some really dramatic ways, throw up obstacles in their path that they'd never have faced, and generally up the tension. It can also move the plot - maybe the heroes go undercover and try to infiltrate the evil empire's army because they just don't have the resources to confront the antagonist head-on. In this sort of situation, reducing the antagonist's power out of some idea that "powerful = Mary Sue = bad" is definitely the wrong choice. I mean, would Lord of the Rings have been better if Sauron had been less powerful and had less of an army?
Of course, maybe the antagonist's power is so extreme that the hero's victory in the end comes off like a deus ex machina, and your overall story loses tension because the conflict is so unbalanced it's unbelievable. Or your antagonist switches sides and suddenly you have to deal with incredible power on the side of the good guys, which is a lot harder to turn into an interesting plot. In that case, you should look at her power level and what you're doing with it more closely - but because it doesn't work for the story, not because "my antagonist is a Mary Sue".
As for the question of "will she be considered a Mary Sue"... well, by some readers, quite possibly. I am astounded at some of the characters I've seen being called Mary Sues in the past. But you can't please everyone, and if you keep your focus on "what will make this story interesting? what will keep up the tension and keep readers turning the page?" those voices are going to be the minority.
