Hello flutists! My high d is in tune, my Eb is in tune, my F is in tune, but my high e natural is HORIBLY sharp. Is this me or my Armstrong 104 (I plan on upgrading soon)? What can I do to fix it?

Probably a combination of both.
Lifting up the pinky in the right hand can help flatten it a bit. Also you can lip it down a bit too.
My E3 can be 20 cents sharp at times if I'm not paying attention too.

Must be your flute, because I have never seen a flute which Eb is not sharp and controllable while E is uncontrollable!

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or it's me? I am the exact opposite in orchestra, I can flatten the E without alternative fingering, but Eb is impossible without alternative fingering. :(

I find the the high E is always a note to think about in order to play in perfect pitch, no matter which flute I am playing it on.

IMHO, there is no such thing as a flutist that does this, nor a flute that does that.
It's always a combinationn of both. Even if you pick two flutes of the exact same model, two different flutists will sound and tune differently.
There is though another factor that come into this matter and this is the scale of the flute. Modern flutes tend to use "corrected" scales, so when you play those known problematic notes, you may note have to do much effort to tune them.
My particular case. I played for 16 years in a 30 year old all silver Standard Muramatsu. I really suffered with high E, specially because this flute did not had E-facilitator nor E-mech.
About 4 years ago, I purchased my gold sankyo and I couldn't believe how easy it was to tune and sound on this flute, made in 1995. It has a High E-Facilitator (donut).
Now, I have another Muramatsu, an EX-III, which I bought two years ago, and that's even more easier to tune than my Sankyo. It has no gadgets, except for the Tsubasa headjoint.
Still, I feel easier to tune my Sankyo when I use my Nagahara head than with the original headjoint.
So, the solutions may be varied. We cannot stablish any rules in this matter, because this is a case to case matter.

My advise is, find the particular solution that works for you. If you change to another brand or model, probably you might have to give some adaptation time until you regain confidence in your tuning.

"problematic notes, you may note have to do much effort to tune them."
I meant "may not have to..."

true story, a student came up to me at the Jupiter booth at a state music convention where I was giving a lecture, she said her flute plays poorly on high E, so she wanted to try a better flute, so she did same problem, then tried a more expensive one, same problem..so I suggested she look across the room up to the corner of the hall and try the E again, lo and behold the E came out beautifully...

it is not always the flute..

Call your teacher or technician, and if they can not repair it, save money and buy other flute, reccomended pearl, yamaha, powell, muramatsu, yamaha, nigahara, arista or haynes, if you can't spend so much money I recommend powell sonare, resona, gemeinhard KGM millenium, vento 800 ebony, and jupiter di medici. thanks, God bless you.
aa!!! I wanna ask the comunity what they think about Gemmeinhardt KGM limited flute, thanks.

i have an armstrong 103 and i close the right ring finger, i.e., low d key, and it drops the pitch about 30 cents which brings it right in tune and actually adds a nice color to the note. make sure you have the headjoint inserted to compensate for the entire tendency of the scale.

i paid $100 used for my armstrong!!!! and the rest of the flute (except high F) plays fairly in tune for such an inexpensive instrument. I have been playing flute for 40 years.