If you are applying for Atmospheric Science, you’ll be applying to Cornell CALS. It will benefit you that you are a New York resident, and CALS is easier to get into than most of Cornell’s other undergraduate schools. They place huge emphasis on fit and interest in the course of study. A 3.04 is low for Cornell’s standards, I won’t lie to you, but if you are truly exceptional at atmospheric science, I wouldn’t say it’s impossible. They admit based on major.
JHU, unfortunately, might be out of reach. It’s a bit more difficult to get into JHU than Cornell CALS. JHU has a transfer admit rate of 10%. CALS wouldn’t be A TON easier to get into, but I think it’s a more forgiving option given your NY residency and the holistic application review.