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The employer should issue you a corrected w-2.   Code J is non-taxable sick pay.   If this is long-term disability and the premiums were paid for by the employer, it is taxable, and the amounts should be in Box 1, 3, and 5.   

If the income is non-taxable, it does not need to be entered.   But if it is taxable, FICA tax (SS and Medicare) should be included.   

Is the long-term disability I am receiving considered taxable?  The answer is YES if the employer paid the premiums, which you indicated they did.   In this case, the income should be in Boxes 1, 3, and 5.  

You can report the taxable income without the w-2 by entering it in miscellaneous income.