The NCAA Champion would soundly beat the Memorial Cup champion, but that is not because the NCAA has better players.
The high end talent in college hockey is distributed between about 8-10 super programs. Michigan, BC, Boston U, Minnesota, UND, Michigan St, Maine, Denver, Wisconsin. I may have forgotten a team or two, but the fact remains, a large majority of the top college recruits end up at one of these schools.
The CHL has 56 teams, and the players are distributed through a pro style draft, where the worst teams are rewarded the best players. So the talent is thinner for team, but the league is more balanced.
So the NCAA would win, but the CHL has better players as a whole.