Well, this isn't the best post I can give you, but I'm going to be a fellow at CHOP in 2006, and I interviewed at both places. Now, I didn't interview at either for residency, but I think Boston is a cooler town, but more expensive, while CHOP seemed to be a bit more of a complete hospital. Plus you only rotate through CHOP, where Boston requires you go to several hospitals. I think that would favor CHOP. Reputation-wise it's a wash, so that shouldn't matter. I think it's mostly how YOU felt about the two places, and where you could stand living for 3 years (and potentially more, as if you meet someone/or already have a family, it can be tough to move).
Feel free to PM me if you'd like. I hope that helped a little.