Is it better for a married couple to pray the obligatory prayer in congregation at home after missing the congregational prayer at the mosque, or for each of them to pray individually?

It is better for you to return to your home to pray with your wife so that you both may attain the virtue of congregational prayer (twenty-some degrees). However, if you find another congregation in the mosque, then it is more befitting to pray with them, because the fundamental principle is that a man's prayer should be in the mosque, and a woman's prayer in her home is better for her and her reward is complete.