Relative differences in CS and Engineering strengths between Yale and Penn are very small - we’re not exactly comparing Yale and MIT here for instance. Both schools tend to have smaller, but very high quality departments, and a range of career opportunities to choose from.
Yale’s culture veers towards the liberal arts and sciences, while Penn veers towards business, entrepreneurship and pre-professional pursuits, though you’ll still find people of all stripes. Perhaps your son prefers interacting with one sort of student body over another. Furthermore, a lot more Penn students tend to be involved in frats/sororities (about 25-30%) compared to ~10% for Yale. I’d also recommend looking at the campuses and residential scene at both.
Lastly, if he is unsure about a choice of major or wants to double major in an engineering and non-engineering field, it is logistically much easier at Yale, since there is no separate College of Engineering to switch into/out of if his interests change.