I disagree that Northwestern isn’t a match for some people. I suspect that it is a match for your son, it would have been a match for my D1 (actually, Naviance had it as a safety, but we didn’t believe that and she didn’t like it anyway). They tend to not play games with admissions. Actually most of the schools you mentioned are matches in that I think the probability of admission is between 40-90%. These would include Tufts, Johns Hopkins, Washington University, Brandeis, Rochester, USC, Wesleyan (larger than Brandeis if I recall), etc. Rochester is almost a safety, they are unlikely to reject your S.
Lehigh is actually a reach, and will likely not accept your S unless he puts a lot of effort into demonstrating interest. It does have Division 1 sports though so if the effort is made, he will likely get in.
Tulane seems like a great safety option. They have early action, though I assume that your S will apply SCEA to Harvard or Yale, in which case, I don’t think Tulane is allowed.
The size thing creates a problem because many schools that would be matches are larger than 5000 students. There aren’t too many 5000 student schools that have division 1 sports that would also appeal to a top student.
I would suggest going larger for the safeties. My D1 who was a tip-top student with stats similar to you S, used Wisconsin as a safety. It was rolling admissions, in a beautiful place, urban, top academics, and she applied at the beginning of September and was admitted by the middle of October. Safety was bagged before the EA applications were due. Pittsburgh is also a potential option for a nice rolling safety. Michigan, though not a safety, has EA and is very likely to accept him. Both of my Ds preferred Wisconsin to Michigan.
If BC is too Catholic, then Villanova will be way over the top! My D2 could tell that it was too Catholic for her without even getting out of the car. It hits you in the parking lot! We had stopped for gas nearby on our whirlwind college tour while driving from to UDel, and were just turning around in their parking lot, LOL!
Another strategy that might be worthwhile is to skip SCEA altogether since it doesn’t provide much of an advantage, and apply EA to Chicago, Georgetown, Tulane and maybe Wisconsin. Northeastern requires no essay so it’s easy to hit that EA also. He will likely have a very attractive acceptance before the Harvard/Yale applications are due, and with a Chicago or Georgetown admission, might actually save him some time filling out applications by eliminating choices lower down the list.