Issa,
You stated in your opening post that you wanted to apply to Stony Brook, which is a 4 year SUNY school (not a community college).
If you are applying to a 4 year school, ylu must pay the fee. If you are applying to schools, which have both Bachelors and associalte programs; Morrisville, Canton, Cobbleskill, you must pay the fee (even if you are applying for an associates program).
regarding, whether you have to pay, it depends. The portal will hold your application until the fee is paid even if yuou applied directly to the school (they can hold the application). you must contact the school directly to have this corrected.