would this be a good science fiction series?

Do you mean a television series? If so, I'd say this isn't a good idea, as a television series would need to involve a regular cast, otherwise it'd just be "here is another vastly expensive remake of last week's plot, but this week it is with Pechenegs instead of Vikings.." Think about series you've seen, most of them involve reoccurring characters which the audience can become invested in. The few that don't usually feature a new story every week and are more of a digest format.

If you mean a series of books, I can see it as a single novel, as there is an entire sub-sub-genre of science fiction novels where historical people fight aliens. I don't see it as more than a one off, unless you luck out and invent a set of aliens which inspire a fervent following, since the aliens would be the only reoccurring characters. I don't see how the "mystery" could be sustained without resolution for multiple books.

What part of this is unique?
There is no "unique" anymore. There are no more original ideas, everything has been done already.
All you have to do is do it really well.

It could be interesting - especially if you do some research and tie it together with ancient religions, myths, traditions etc.

As with all writing, though, whether or not you can pull it off will depend on how well you write.

Not at all, I'm afraid. Such a series would very quickly devolve into dragons.

The Vikings were not an ancient civilisation.

Yes.

Actually my concept is someone from the future being thrown into the past. In the past they are a minor character, AKA Merlin, who just knows how to make things that can't be made in the 5th or 6th century. Obviously a variation on the Arthurian legend,
As for aliens , eh, eh , merlin is not one but has conversed with as few on a very conversational level.

Sure - you could call it Star Trek or The Outer Limits. Both of those were largely human meets alien.