You can't go wrong with any of these programs. The new work hours are going to change the training at almost all of the top tier programs. I can really only speak to Hopkins.
Hopkins is traditionally thought of as one of the most rigorous and one of the most autonomous. On the O (general wards) you are the only one seeing the patients overnight and during the day, you are the one making the decisions. For the most part, you can write your own ticket coming out of Hopkins.
The program is very heavy on Cards and Pulm/Critical care and because of that about 1/2 of the residents go into Cards, 5ish go into Pulmonary Critical care each year. Each year a few go into ID, a few go into Onc and a few go into GI. Very few go into Rheum or endocrine. This year we have 1 person going into rheum and that is a lot. The kind of people who are attracted to Hopkins are also the ones attracted to Cards. The cards teaching just draws people in and converts them to cards.
I don't know too much about the boston programs except what I learned during interview day last year- which wouldn't help you all that much.
I don't think you can go wrong with any of those programs. I'd go with whichever program you feel most comfortable with.