Get your taxes done using TurboTax

You are able to file using the Married Filing Jointly filing status with your spouse's ITIN. 

TurboTax will accept the ITIN in lieu of the social security number and should accept it for efiling as well.

TurboTax can only be used by individuals electing to be treated as residents; it does not ask any questions about citizenship or nationality.

Your spouse's income can be added under Wages and Income, Less Common Income, Other Miscellaneous Income, Other Taxable Income:

Reporting the amount of income you have stated in this manner will not generate any questions that need to be answered regarding the geographic source. 

You are correct, income earned in Cuba cannot be excluded from US tax (USNB Guantanamo Bay is not considered to have been earned in Cuba).