You should compare courses offered in those majors. MIT is a huge name in STEM but Yale can afford to spend a lot on your education and there are advantages to being a relatively rare CS or EE major in a soft science/humanities paradise.
If the MIT course offerings blow Yale away and cost is close, and you are ok with MIT’s dorms/food/culture, MIT is probably the better choice.
But if Yale competes in terms of offerings, and cost is close, I think that makes the decision more interesting. It’s Yale – nothing they offer is less than at least pretty good, and even in STEM Yale will open doors. You certainly will get plenty of prof attention.
Visit both and get your gut feeling. Kids at MIT reportedly have fun despite the rigor and Yale is known for its residential college system. If you were accepted by both, you’re very lucky.