My personal opinion: If your goal is to play some ECHL or minor league hockey, even AHL hockey, in your 20s, it's better to go play college hockey, get a degree and then after 4-years of the college hockey experience jump to the ECHL or AHL and see how far you can go. At least then, you'll have a college degree to fall back on when you decide to hang 'em up.
If you're a legit NHL prospect the decision is a bit trickier, both are great options to get to the NHL now but major juniors and college hockey offers slightly different experiences to get to the same goal.
Also depending on your age (i.e 15-16), it's my opinion that you don't have to decided MJ or College Hockey right now, go play NAHL/USHL or in the higher level/best scouted CJHL leagues and keep the NCAA eligibility while gaining NCAA DI interest then make an educated decision around 17-18 yrs old.