Before I go further, I’m sorry for your loss. Since you and your spouse lived apart for the past two years, the IRS will allow you to file using the head of household filing status. You can continue to do so for 2016 and for the years going forward.  You could also choose to file as married filing joint for 2016, and as a qualifying widow for 2017 and 2018.

If there are debts such as back Federal taxes, child support, student loans, or other non-tax Federal debt associated with your deceased spouse. You would need to file an injured spouse claim if you choose to file a joint return for 2016. If his mother claims him as a dependent for 2016, filing a joint return would prevent you from claiming your children as dependents on the joint tax return. These issues may make filing a joint return for 2016 less attractive.

However, for 2017 and 2018 filing as a Qualified Widow would be recommendable because the issues mentioned in the paragraph above would not apply. The qualifying widow status allows you to claim the benefits of filing a joint tax return without the joint liability and dependency issues. See this link for a full description of the benefits of filing as a Qualifying Widow with Dependent Children