Hey,
Those are definitely two very different fields. Most of us here would agree that iSci is awesome, but that's mainly because it suits our interests, our style of working, and most of us like the solid and wide background that iSci provides.
In your case, I'd really take a look at which subject 'fits' you better. I know that nanotech eng. at Waterloo is a great program, I have a couple friends there who are really enjoying it. From what I understand, that subject itself is very interdisciplinary as well. Within iSci, to be clear, you are unable to take engineering courses.
The two things I would look at most in order to make your decision is if you're more of an engineer or more of a scientist, and also compare Waterloo to McMaster, to see which university suits your needs more.
Every decision is tough, don't be persuaded by the biases and opinions on this forum, because I know both programs are great, and really choose the one that feels more right for you!