GPA worries!! Please help!

[Elle07]

hi,
i've begun to prepare for the graduate school admissions process: i've written my written sample (that was given a fairly high grade), got 3 letters of recommendation, scored a 330 on my GREs, and am currently holding a GPA of 3.9 (last two years). however, my GPA for the first two years was not as stellar: i held a 2.9. 
now, i'm terrified that my GPA from my first two years will come back to haunt me. if i were to combine the two GPAs i'd get an overall GPA of 3.4 or 3.5. do you think a schools like Columbia University, University of Chicago, NYU, or dare i say it, Harvard would accept me?
the only reason i'm so scared is because if i were to apply for the graduate program at my school (University of Toronto), the admissions office would only look at the last 2 years of my undergraduate program. whereas most of the universities i've checked in the United States look at all 4 years. 

thank you very much!