Hi and welcome to JustAnswer!
So far - your total estimated gross income will be:
Wages - $40 / 12 months * 6.5 months = $21,670
Unemployment Benefits - $8,866
Your spouse's wages $90,000 - $3,750 (401K contribution) = $86,250
Minus student loan interest deduction $2,500
Total - $114,286
Assuming standard deduction - your estimated federal income tax liability is $15,460. Because both - you and your spouse are working - your better to use status on W-4 form "Married, but withhold at higher Single rate" - http://www.irs.gov/pub/irs-pdf/fw4.pdf
If your spouse will use two allowances - her federal income tax withholding would be $15,312.
If you will use two allowances - your federal income tax withholding would be $1,400.
So you may expect - $1,200 refund when you file your tax return.
So I suggest you both file your W-4 form using status "Married, but withhold at higher Single rate" with two allowances. The same filing should be for IT-2104 form.
Customer: So we both should claim two allowances on each of our W-4s? As well as on our IT-2104s? The bottom line is for each of our W-4s we both claim two allowances on our respective W-4. One our NYS withholding we again both claim two allowances. Are you sure we can claim both two allowances on both of our W-4s as well as for IT-2104?
LEV: That is correct - according to estimation above - you will due $1,200 refund when you will file your joint tax return. I do not have NY calculator - but assume there will be $300-$400 refund as well.
Customer: But based on the above information we won't own for NYS right?
LEV: That is correct - you should not owe any taxes but will have a refund instead.
Customer: For my wife to make these changes should we print out new withholding forms for fed and NYS and fill them out and submit them to HR or should we first contact HR to get the forms from them to edit?
LEV: If your spouse filed differently and wants to change withholding - she should submit a new form.
Customer: Okay, thanks.
You may print forms if you want
Customer: Okay, thanks
LEV: You are welcome.