Should I switch from an M.A. to an M.S. program if my department allows me to choose?
In general, I believe your assessment is correct—for scientific disciplines where both an MA and MS are possible, the MS degree is usually regarded as more rigorous than the corresponding MA degree.

That said, whether you should switch is a matter that requires some thought. Does the change require you to complete more courses? Will there be any impact on your expected graduation date, and the cost of getting the degree? If not, then I would definitely switch. (Moreover, since you already have an MS in engineering, there's no point in getting an MA afterwards. If you didn't have a master's, you'd need to figure out the relative advantage of finishing faster versus the more rigorous degree.)