File joint. If you file separate, you automatically disqualify yourselves for tax credits and deductions you get if you file joint. For example, if you file separate you automatically do NOT qualify for the child tax credit, child care credit, and earned income credit.
Basically, for a married couple to file separate, you will almost always pay more in taxes than if you file joint.
Also, he did not have health insurance after mid April last year and I of course lost benefits when I dropped to part time.
So a penalty will be assessed, and it has nothing to do with how you file. If there's a possibility to qualify for an exception to the penalty (either one or both of you) the program will know based on the data you enter, and offer you options to either negate, or at least reduce the penalty.
