How sharp are they, and are they - C# through F - fairly consistent in their amount of sharpness?
Are you talking 2-3 cents or pretty horribly sharp? What horn is it? (not proof of anything either way but the Yams, Yanis and Selmers etc are going to be more trustworthy of being 'within a tolerance').
I think that you should determine (if you haven't already) that the mouthpiece is pushed onto the sax in the optimum place for tuning in general. I think most of us, me included, find that the mouthpiece should be pretty high on the cork for soprano - depending upon the width of the cork!
If the rest of the horn has consistency and these high notes are the exception then there are only three possible answers:
1) they really are sharper than the rest of the horn;
2) you're subconsciously tightening up the embouchure and/or the throat/tongue position;
3) that you're playing the rest of the horn under pitch but not these high notes.
Let's start with 3). Yep, unlikely. Your ear should tell you if the note is centered. Depending on how experienced you are you'll be able to tell if a note is not played with the right integrity, not centered. Hearing a note that is strangled by over-biting or not having a large oral cavity is probably easier. Let's assume unlikely...
2) If you play a top F, how far can you lower the pitch with tongue position/throat/lip? You should easily be able to take up the slack, and then some. So, the correction from you should be easily possible, but if the sharpness is in the region of 5 cents or more, I'd want to know if life could be made easier.
1) Do the keys open excessively and vent too much? Extra cork under the key stop will take the venting lower and there may well be some small gain here. Probably not a fix, but definitely some help.
I've just looked at your profile to see that we're talking about a Yani 991. I've had two Yani sopranos - a 991 curved back in the 1990's and a straight 901 recently. I can't get on with curved sopranos, wrong shape for me in the way it hangs from the body. Great horn though. The 901 I found to be thin and a bit small. I never had intonation problems that couldn't be conquered.
As a first experiment try mouthpiece positions to see if one position produces a decent tuning between the three E's. If there is some success, where is the horn with regard A=440?
Flatness is the true enemy, as there is very little affectation we can have towards sharpness as long as we are blowing properly etc. Sharpness is fairly easy over most of the horn, but big local differences are nasty.
Let us know the outcome of your experiment - better still, post an audio file of the problem area and the other registers as a comparison.
Cheers
P