First, 3.9 is not low unless your school has grade inflation or is highly competitive. Based on the scores you have I hope it’s the latter. If it’s highly competitive you should look at Naviance or talk to your GC about prior students like you.
9% outside the top 10% of school for ND. https://www3.nd.edu/~instres/CDS/2015-2016/CDS_2015-2016.pdf
Chicago and MIT don’t have D1 athletes. Nothing more to say.