As a J1 and J2 visa holder, you are a nonresident alien and have to file form 1040NR. 

TurboTax doesn't support Form 1040NR: U.S. Nonresident Alien Income Tax Return, but we have a partnership with Sprintax offering a nonresident tax filing solution to our TurboTax customers

Thank you for your responce.

I have been using Sprintax for 2 years. But after 2 years on J-1, I am a resident alien.

So have to file using TurboTax.

But as my wife cant get SSN what should I do? Is she still Non-resident alien? Married filing separataly is correct?

If you have SSN and are treated as resident alien, you have a choice to file Married Filing Jointly or Married Filing Separately. If you elect to file jointly with your wife, you will need to apply for an ITIN for her and you will also need to report all of her income.  By filing jointly with her you will be making an election to treat her as a resident alien for tax purposes (just for tax, this doesn't actually make her a resident alien).