I can think of one unique thing about Upstate. It has great computer technology use. All lectures are recorded, and made immediately available online as streaming videos. Also, all powerpoint presentations used in lecture are posted. In theory, you do all of your daily classes from home. (although not advised).
Your main decision is whether to take a state school over Jeff or BU wich are nicer places and more well known and more expensive.No real advantage to Upstate over Downstate unless you want to get away from NYC/Brooklyn and experience a more rural setting.