"Obviously the gold standard for high academic college athletics is the Ivy League... what I'm trying to get a better handle on in helping to advise son is how schools in confs like NESCAC and others stack up, baseballwise, with the level of play at the Ivies."
Soylent Green, taking this as a main focus for your question and guidance for your son, I think the comments on schools as opposed to conferences makes sense. For instance, the top Ivy baseball schools at this point, like Columbia, Dartmouth and Cornell will/should and do play the game at a level which is measurably higher, over the course of a season, than the top programs in the conferences you have listed. However, if we were to take Columbia just 5-6 years ago, or those toward the bottom of the Ivy's, the quality of play often won't be measurably better than at the very top of the conferences you have listed, when the top D3 programs in the conference compete against each other. The other aspect of this is while the top D3's competing against each other won't be distinctly different from the lower level Ivy teams competing against each other, a game between the top and bottom NESCAC programs, for instance, will likely be less competitive with a lesser overall quality of play from the top Ivy and bottom Ivy program. In other words, the bottom of a D3 conference is farther from the top than in the Ivy leagues, speaking in generalities.
Finally, speaking in generalities, the top recruits at the top programs in the D3 conferences you have listed will likely be on the list for recruiting with many of the Ivy's. However, they probably would not be the #1 or top recruit at a position. That being said, if they end up at the upper 1/2 of the Ivy programs, they will have a bigger battle for any playing time as a freshman and possibly even a sophomore. If they "settle" for the top level D3 program, most will probably be battling for playing time immediately.