Go to StonyBrook. Like other posters said, Rochester is a great school, but is not worth that much extra money. If you think about it, it would be about double the price to go to Rochester. At Rochester, you have to pay 40k in tuition alone, plus money for housing, food, traveling, clothes, etc. At Stony Brook, you would pay 18k for tuition and that's practically it. You don't have to pay for housing or anything because you live on LI, and you can live at home when you do your rotations bc the rotations are probably around the area that you live. Think about it: 250k in loans at Rochester or less than 100k at Stony Brook?
I am a little bias here bc I live on LI and want to go to Stony Brook, but do the math. There is no comparison.