My GPA is a 3.9, and I have quite a few extracurriculars, but I haven't taken the ACT yet. I want to apply early decision to Cornell as an engineering major - what score should I aim for to be relatively sure of admission? Should I focus more on the Math and Science sections or will they pretty much just look at the composite score?
Your goal should be a 34 on the ACT if you want to give yourself the best chance of acceptance. A 34 is the 75th percentile score for admitted students at Cornell, so if you score a 34 or higher, you will be considered a very qualified applicant. According to most sources, Cornell does superscore the test, but you should call the admissions office to verify this. Provided superscoring is a factor, if you don't get a 34 composite score the first time around, you can always take it again and focus on improving sections where you didn't score as high.
At this competitive of a school, all of your section scores need to be extremely high, so I wouldn't devote a disproportionate amount of attention to Math and Science unless you initially have more trouble on those sections. Cornell will focus primarily on your composite score.
Source: https://www.prepscholar.com/sat/s/colleges/Cornell-admission-requirements