I believe common sense should tell you that once you get beyond a certain level in the minors, the teams are without a doubt better than the best D1. After all, the minors are composed of the best of these players from years before. They are also comprised of the best players in high school from back when these college players were in high school who have made it through a couple of years of pro ball.
However, I am not convinced that the lowest level of the minors is better than the best D1. The reason is that, while there are some outstanding former college players, there are a lot of very young players labeled with "potential" .
Anyone who is around the game, knows that professional baseball drafts on "potential" and "projection". While it serves them well eventually, the lowest level is filled with these players who are bigger on "potential" than actually "have game".
I'm sure we've all seen guys who get drafted ahead of guys we know can play the game. Unfortunately these guys either couldn't quite run quite fast enough, couldn't throw quite hard enough, or weren't quite big enough. The only thing they can do is play the game.
So until these pro players who are thought to have so much "potential" and "projection" are weeded out, I'll put my money on the top D1 team who are filled with guys who we know can play and compete.