I recently took my first two AP tests as a freshman- AP US History and AP Computer Science Principles. I earned a 5 on the AP United States History test, but a 3 on the AP Computer Science Principles test. I really want to attend an Ivy League/top school, but am worried that my score of 3 will reflect negatively on my application. Is that the case? Do colleges even look at AP scores? I received an A in both classes on my transcript. Thank you!
I don’t think that you should be worrying about Ivy League or highly rated universities at this point.
There are a very large number of very good universities. You can be very successful with a degree from any one of at least a couple of hundred universities and colleges in the US and as many elsewhere.
Do what makes sense for you in high school. Then look for a university that is a good fit for you, and that you can afford.
The Ivy League schools, and equivalent schools (MIT, Stanford, Chicago, Caltech, …) are a high reach for the very strongest students, and out of reach for most other students.
That being said, I do not think that a 3 on AP CS principles as a freshman will make much if any difference to your chances.
AP scores are predominantly used for placement, not admission.
At a Q&A session with an AO at a top 25 school last week, a parent asked if a good Math SAT score and a 5 on Calc AP meant his child didn’t need to take the ‘recommended’ Math Subject Test because the child had shown math capabilities.
The AO said “we don’t even look at AP scores”.
You have a long road ahead of you, and if you spend the next 2.5 years anxious about ‘ruining’ your (tiny) chances of getting into a specific school you will miss a lot of important (and good) things.
Read this, believe it, live it:
https://mitadmissions.org/blogs/entry/applying_sideways/
Re: your pros/cons on “Ivy League” thread, imo the biggest cons are interrelated: the idea that the label makes them similar and magically better than genuinely dozens of other schools (in terms of academic rigor, resources, college experience, etc). If you lovelovelove Dartmouth, would you feel the same about Columbia? Cornell v Brown? UPenn v Princeton? Do you know the difference? There is another thread on CC right with a student ranting about how terrible Columbia is and how much she regrets choosing it- which she did ‘b/c it was an Ivy’. Columbia isn’t terrible- it’s just terrible for her b/c it isn’t a good fit, but she couldn’t see that through her prestige googles. You don’t want that to be you.
If you are going to be an early college shopper (I had one of those), start with things that you think might be important to you- a subject area, a region, a student experience element such as sports, whatever- and identify some colleges that match that. Identify them in a range of levels- from super competitive to state u. Research them, and them make and re-make the lists of possible colleges.
And don’t tie yourself (out loud or to yourself) to any of them (among other things, that makes it easier when admissions results are coming out). Leave yourself room to grow and evolve. My early shopper collegekid went through many, many lists before settling on her definite, final list in spring of Junior year. She had visited them all, had spent the night and/or sat in on classes at most of them (including the ED one she loved). Four months later she applied to a completely different list of colleges and ended up supremely happy at a place that wasn’t on her list until the August before senior year. 
It’s a time of growing and changing- give yourself room to grow.
ps, you don’t have to report your AP scores, a 3 is not going to be a deal breaker, and there is a general view that after 6-8 APs competitive colleges stop being interested (unless it is part of what is required at your particular school for the GC to tick the ‘most rigorous’ box - you can check with your GC on their policy).
APs aren’t really used for admissions, just for placement/credit.
For example, Stanford says:
Students currently enrolled in AP courses are not required to submit AP scores as part of our admission process. AP scores that are reported are acknowledged but rarely play a significant role in the evaluation of an application. Grades earned over the course of a term, or a year, and evaluations from instructors who can comment on classroom engagement provide us with the most detailed insight into a student’s readiness for the academic rigors of Stanford.
http://admission.stanford.edu/basics/selection/prepare.html
Let me state clearly: we do not admit students solely because of their AP courses/scores. There is no minimum or recommended number of AP courses. AP scores are not part of an admission formula… What we are saying is that, despite what you may have heard, college admissions isn’t a game of whoever has the most APs, wins.
https://mitadmissions.org/blogs/entry/on_aps_1/
Also:
Do not think 'Every point I get off of a homework or test is a point away from going to Harvard."
Think: “I need to do my best, and there will be a college that is right for me when I graduate.”
Do not think “If I don’t go to an Ivy League School/Top20, I am doomed forever.”
Think: “No matter where I go, I can bloom where I am planted. I can get involved and shine.”
Do not think: “My life is over…the kid in my math class is taking 20 APs and I am taking 5. I will never succeed.”
Think: “I need to challenge myself, but only to the point where I can still do well.”
Do not think: “My AP Scores as a freshman(!) will doom me forever.”
Think: “It is awesome I am able to take college level classes as a freshman and do well. I need to challenge but not over challenge myself.”
Not sure why a kid asks about Ivies and anyone insists adcoms don’t care about AP scores. Most especially, if OP had issue with a stem class and is a stem wannabe.
OP needs to realize he/she has time to take more AP, get top grades and top scores. Then, maybe don’t send the CS score. APCS courses are no magic. Some don’t get far. And much, much more important are math and lab sci core classes.
You don’t get into an Ivy for dreaming. Learn the breadth and depth of what they look for. Make a feasible plan.