JCG
All great schools. But, big time athletics (and those are all baseball powerhouses) impact academics more then lower level athletic programs (e.g., major selections, classes missed, etc.). (Except Stanford.)
When a program has legitimate expectations of a possible CWS year (and every program you listed does), priorities of coaches and players are a bit different when it comes to academics. Sixty game (potential) seasons, seasons that begin in February and end in June, maximum practice times (and pushing that to its breaking point) do impact academics when compared to a forty game season beginning in March and ending the first week of May with less time mandated for practices, and total formal practice shut downs during things like study weeks, mid-terms and finals.
While there is some overlap in raw academic potential (as demonstrated by HS performance of recruits) between those schools, Ivy League rules dictate where the academic bar is set to be admitted. That academic bar is higher then the fine schools you mentioned.
Also, in certain industries, the Ivy League schools are job factories. It's not a single element which, again IMO, tilts the scale for most towards the Ivy League; it's the cumulative effect of lots of little factors (financial aid, employment opportunities, somewhat reduced athletic requirements, less pressure to produce right out of the box).
The obvious trade-off is the quality of baseball. Ivy League baseball is fine - but not nearly as good as those other schools.
Sounds like you know the baseball culture far better than me. I was just pointing out several other D1 schools that are, like Stanford, both top baseball schools and cited as among the top 10-20 most selective and/or highest academic schools in the country.