Hi Khaya,
Both are great programs, but they are different in a number of ways. MGH is a much smaller program, which has both benefits and negative aspects. You'll get more of a feel for this as you go on interviews. That said, it still has exposure to very complicated patients, so you're not missing out on much.
Children's has a better academic reputation, based on the amount of research that comes out of the hospital and the fact that it is a referral hospital for, in some cases, patients from all over the world. Whether this translates to better resident training is a subject that different people have very different opinions about. Again, you'll have to get a sense for how important that is to you.
Lastly, lifestyle-wise Children's is, I think, a harder residency, in that patient loads tend to be higher, patients a little more complicated, and there is less call-free time. There is no way I would call it malignant, as the residents are generally happy there and the administration is very friendly and supportive. But if the most important thing to you is maximizing your free time, it might not be the best option.
With all that said, I don't think you can go wrong with either program. People tend to do extremely well getting jobs/fellowships coming out of both, and you'll get great training at either. It's just a question of which seems to fit you better.