My wife is looking for works of science fiction which feature characters (esp. protagonists) who are female who are excellent human beings in a way that is irrelevant to the question of whether or not they are excellent women.
Could you define your terms?
I don’t think it would be helpful to narrow things down further than I have in the OP. We’re interested in whatever people suggest that they think fits the definition given there.
(In other words, we’re much more interested in how the works suggested define these terms (if at all).)
For “excellent human being” you could substitute “human being in an interesting situation” as well. So basically, books where the protagonist is a woman, but it is unimportant in the book whether she is a good specimen of woman or not.
I’m a little fuzzy on what you’re asking - are you saying in other words you’re looking for sci-fi stories that depict positive; non-stereotypical depictions of women? I.e., women who three-dimensional characters and not just adolescent male fantasy objects?
Offhand, I would suggest reading some of Octavia Butler’s works. Start with “Parable of the Sower.”
Cordelia Naismith by Lois McMaster Bujold.
…are we talking “excellent human being” as in “good role model,” or as in “Übermensch”?
Dr. Susan Calvin
Arkady
Podkayne
There are two certain ways for a fiction author to engender (heh, heh) criticism from “feminists”: one way is never, ever to use female characters; the other way is to use female characters…
Captain Mazian in Downbelow Station
The Star Trek novels feature many strong women who rarely exhibit any femininity. You might check some of those out.
I enjoyed reading all of Jack McDevitt’s books about Priscilla “Hutch” Hutchins, even tho the science aspect is fairly weak in most (all?) of them.
The Engines of God
Deepsix
Chindi
Omega
Odyssey
Cauldron
Of course, there’s always Robert Heinlein’s Friday.
I loved the books about the living moon of Jupiter, Gaea, by John Varley: Titan and Wizard and Demon. Cirocco Jones rules!
Dana Scully, until about season 7. 
In fact, any woman written by Morgan and Wong, including Kylen Celina from S:AAB.
Velasquez?
Except for Friday being a complete idiot, and emotionally dependent on pretty much anyone who comes near her.
Iain Banks does some decent female characters (i.e. emotionally balanced, independent, capable and “good” in terms of the story arc). Djan Seriy Anaplian from Matter, Lady Sharrow from Against A Dark Background.
That would certainly be responsive to the OP.
Just as in, a good specimen of humanity.
In other words, women who are such that their being a good human doesn’t depend on their being a good woman. (Though see a subsequent post–“excellent human being” isn’t necessarily what she was after.)
On the other hand, though, that approach to “excellent person” starts heading into another problem…
The four women of Firefly are all strong female types and “excellent people” in very different ways. I suppose Inara might possibly fall into the “good woman” category but frankly I’m still somewhat baffled by what the OP considers the difference to be.
Honor Harrington series by David Webber.