Do you know what college(s) are your safeties? Are you comfortable with attending them?
I am going to be blunt here: I think there’s a huge disconnect between your college aspirations and your desire to homeschool.
In the context of elite college admissions, I don’t think you have given very good reasons for wanting to homeschool: “I can’t both be first in my class and also achieve my full potential senior year” – “If I stay on for senior year I’ll have 4 APs and basically no time to pursue any of these projects while also applying to colleges.”
The students you are competing against for admission have done exactly what you say you can’t do: they have continued to take a full load of challenging courses while at the same time being actively involved in EC’s, athletics, or outside projects.
That doesn’t mean that it’s a bad thing to opt for homeschooling: but you’ve got to make a choice. If your goal is to attend an elite college…then I think you need to finish the path you are on. It’s true that some students who have followed a divergent path have benefited in college admissions because of the way they stand out. But they didn’t start in senior year – and I don’t think that most of them have elite college admissions as their goal, even if some of them do manage to get admitted to elite colleges.
If you want to work independently and take charge of your education, then I think you should rethink your college choices. In addition to finding a safety that you are happy to attend, you might start looking at colleges that seek out independent learners – for example, Hampshire, Sarah Lawrence, NYU Gallatin. (Though of course you need to be also aware of finances – your own parent’s ability to pay, eligibility for need based & merit aid). Or perhaps look at match/safety schools that are known for politically active student bodies.
That doesn’t mean that you can’t still apply to Yale or top LAC’s… but you need to be accept the reality that choosing to homeschool is likely to significantly diminish chances of admission. Obviously the odds are against admission in any case – that is, staying in school for your senior year is no guarantee of admission. But it puts you in the position of having to explain something odd about your school record – and again, the reasons you have given here aren’t the sort of thing that will resonate with college admissions.
So bottom line - you need to get your priorities in order. You don’t have to stay on the path that others have set for you… but you have to accept the consequences of deviating. And bottom line – at this stage, it probably is not going to help with elite college admissions.
In other words, the answer to your question, “Will homeschooling my senior year if I’m first in my class hurt my chances at top schools like Yale?” is that you should assume that the answer is “Yes, it will.”
If you are looking for someone to tell you anything different, then you probably don’t have the right mindset to follow the plan you are proposing.