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However, in act 10 of Sailor Moon, Queen Serenity's image that appears to Sailor Moon and the inner senshi while on the moon states that she was the one who woke Luna and Artemis so they could watch over the senshi, which makes it seem like she would likely have been the one to guide them (especially Artemis) after both were awakened. On the other hand, the lack of power to fuel Queen Serenity's image that caused her to disappear in front of Sailor Moon and the others and Mina and Artemis's very freindly relationship with the "Boss" gives me more reason to doubt the theory, and overall I don't think the "Boss" was really Queen Serenity. 

I believe this was the original intent, and the prior relationship between "Boss" and Artemis could be explained with the energy required for different types of communication; they stated that the Moon's Supercomputers lasted, and the supercomputer had QS's consciousness within it - the supercomputer was what was sending messages to Artemis and acting as "Boss," and this "Boss" intelligence lasted up until the team went to the Moon and the computer used what was left of its energy store to produce a hologram of Queen Serenity, so Princess Serenity might see her mother and her mother might 'see' her. 

Correct me if I'm wrong, but don't we see a slight silhouette at some point of "Boss" on the computer screen and it kinda looks like Q. Serenity? Or am I getting confused with the V silhouette we see in the 90s anime at some point...

I don't think "Boss" was ever shown. I'd have to double check though.
you might be getting it confused with Crystal when Luna sees Sailor V in the base.

Yep you are right. I just went through the volumes and the scene I was thinking of (when Minako first goes to the arcade) they don't show boss. So yep, I was confusing both 90s anime and SM manga. xD

So it WAS the spirit of neoqueen serenity, though how the moon had a supercomputer in the first place is beyond me and probably a good idea for another discussion thread lol.

I'm pretty sure it was hinted at eventually that it was the spirit of Queen Serenity.

There are two options here:
1. The "Boss" is the consciousness of Queen Serenity as seen in Act 10 of Sailor Moon. This makes a lot of sense to me because the speech bubble for "Boss" is always drawn kinda digital-ish? I don't know how to quite put it. It also just sorta fits.

2. The "Boss" is Luna. This makes less sense than the other one, but the implication is that Luna and Artemis were awoken at the same time. But there's a whole bunch of problems with that, because Luna didn't know about Princess Serenity (and I'm pretty sure "Boss" and Artemis did, I'm a little fuzzy on that). And Luna wouldn't know all the things "Boss" did.

The problem is that we never hear the "Boss" referred to as anything other than that title. They're never even given gender pronouns. I just thought of another idea too: "Boss" could be the scrapped Diana the Moon Fairy idea too, which explains why we never get any explanation on who they are.

In the fourth arc, the kaleidoscope speaks to Usagi before it becomes her sword. So the idea of randomly sentient inanimate objects is not a foreign concept in the series. That was never explained either. It may well be that Boss was the pen, self-existing. *Shrug.*

That means Boss is dead now. XD