Sumesh:
Did your visa status change when you went on OPT? If you are still on a F-1 visa, then you file Form 1040NR with a Schedule C to account for the income documented by the Form 1099-MISC.
Further, if you are still on a F-1 visa, you are still an exempt person, which means you do not have to pay Social Security and Medicare taxes. You should go back to your employer and ask that these taxes be reimbursed to you. If they refuse, get it in writing, as you will have to submit it to the IRS with Form 843 (and a few other pieces of documentation) to get the taxes refunded. See IRS Pub 519, page 46.
For the state of Ny and NJ, you have to file tax returns for both states to report the income earned in each state.
BTW, this can be rather complicated. I recommend you get professional tax help!
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