What quality of University should I shoot for (USA)?

I'm entering the part of High School where I begin to look at Colleges, and they being to look at me. I have excellent test scores, so I have been getting mail from top notch schools like NYU, UPenn, Georgetown, Cornell... etc. However, Due to some extenuating cirstances (60 days sick Freshmen year, My sister's suicide attempts Sopre year) My GPA is at a 3.5 Weighted... far less desirable than what these colleges look for. However, Junior year so far I have about a 4.4 Weighted GPA. Should I bother applying to better colleges, or do they only care about the facts? Any tips opinions or help would be much appreciated =]