I completely agree. Reputation will not matter, even for getting whatever residency you want. Remember, people from all schools get residencies, even in competitive fields. People will tell you that you will get a better residency from Hopkins, but what is Better??? Does "better" mean a better name residency? The only thing true about a school and residency is what is known as "home school advantage"? What does that mean? Let me clarify...
When you go to a med school, you have an abnormally high chance of staying at that med school, for two reasons. #1) They like you - you got to know them 3rd and 4th year and they know what you can do. #2.) You like them - something that people don't get. You have been living in a place for 4 years, you are comfortable there, you realize that you can do whatever you want there, and you have probably created a life in the area that you don't want to move away from, so you stay. As a result, in the Residency Match process (called MATCH for a reason - your choices are equally weighed against the hospitals' choices), most people stay at their medical school's hospitals. Outside of the home school advantage, there is minimal gain from going to a higher rep school - regardless of rep, most lower-rep schools place about the same amount of people in other schools as higher-rep schools. Which means, even if you think you'll move in 4 years, ask yourself, if you didn't move and instead were to remain living in an area for 8-10 years, where would you pick - the answer to me is obvious (NYU).
Also, to be a good doctor, you should consider what kind of environment will make YOU a good doctor. Do you want an ultacompetitive academic environment where the professors are more focused on disease processes than helping the patient, or a curriculum that is more focused on helping the patient than knowing the nitty-gritty disease process (schools can't even do both, cause there is a lack of time issue there - do you focus your time as a school to learn the processes in depth, or learn about how it appears clinically to depth. Don't think that better rep schools do it any better - in fact, at Harvard from what I hear, their New Pathway curriculum teaches to the latter method whereas their HST curriculum teaches the former, and long term studies have shown that PBL-vs.Lecture have no sigificant differences in them in making a better doctor. Therefore, it is up to you. See which kind of student body you relate to more, as you will probably do better among similar personality types since you are happier. You are in your 20s or 30s now - pick a school that makes you happy during these precious years. Seriously think if you are REALLY going to have an academic life in the future, where you are devoting much of your time to trying to write papers, obtain grants, do experiments, .... AND then practice on the side. That leaves very, very little time for yourself and your family, if you are considering one. You are only getting older - start making decisions that are life beneficial, not just CV beneficial.