First and foremost take everything you read on this board or others under heavy scruinty including everything I say. Anonymous internet posters myself included usually have no idea what they are talking about, but I have been through law school which gives me a modicum of credibility, but nothing more. Every law student and lawyer had a different law school experience and you will find plenty of people that loved attending these schools and plenty of people that hated them. Whether you love or hate your experience is largely up to you and there is no accurate way to predict how it will turn out.
In response to the actual question there are some real factors to consider.
1) Location Chicago and Boston are in complete different locations probably not a news flash to you, but the city you go to law school in makes a big difference. If you have friends & family in Boston or Chicago that should play a big role as those connections will be good support through law school and those relationships usually help you get your career started. You are also going to get an apartment, probably start a romantic relationship if your not in one already, make friends, and just build roots in Boston or Chicago over three years and odds are you will stay there the rest of your life. 0L's really don't think location through enough. It is true that people do just move back home, but when you have made many friends possibly started up a relationshp moving across country is not easy especially if you have a a lot of debt.
2) Cost. This is always something to think about and be wary of scholraship conditions there is a 66% chance you will not be in the top 1/3 at JMLS. Every student at every ABA school is smart, hard working, and sincerely believes they will be in the top 10%, but 90% are wrong. This NY times article does a good job explaining it. http://www.nytimes.com/2011/05/01/business/law-school-grants.html?pagewanted=all
A major thing the students in that article did wrong is they did not ask questions. Do not make the same mistake 28,000 over three years is nearly 90,000 dollars on the line. If you had 90,000 on the line for anything else you would ask some serious question and this situation should not be treated any differently. You should also negotiate for better conditions and also don't be afraid to tell New England about your scholarship offer at JMSL they might throw you some money. That is what I did and it got me an extra 15k in scholarship money I did nothing more than ask. They will not revoke your acceptance for asking they have determined you to be a qualified applicant and they want you in their seat, but if your willing to silently sit by and pay full price they won't encourage you pay to less. Remember above all else that law schools are a business and your a customer. Be reasonable and decent to the adminstrators, but if you don't say anything they have no problem taking your money.
NEVER plan on transferring. If it happens that is great, but as stated before there is a 90% chance you will not be in the top 10%. Even if you are in the top 10% you make a lot of friends first year and you get roots dug in and there is a strong likelihood you will not leave. If you end up in the top 10% then think about it, but odds are it won't come up so plan on transferring.
4) Subjective feeling about the school.
From your post it sounds like you really enjoy NESL. That is really something ot think about every school has a culture and a feel to it and if there are activities there that speak to you that is something to consider. Back when I was choosing some schools felt right to me while others did not. If you love the professors, admins, programs, and everything about a particular school it might be worth the extra money.
Certainly visit both schools and see how you feel if visiting is not an option in Chicago I would recommend not just showing up first day of school and seeing how it goes. This is a very serious decision.
5) The reality of legal education is that in reality it is all the same. Whether you attend JMSL or NESL you are going to take torts, contracts, civ pro, property, crim pro, and when it is all done you will join people from Ivy League and T4 schools in BarBri where you pay an additional 5k and stress out together. There are electives which make a difference and the clincials you discussed may be different than at other schools, but the core educaiton is the same at every single law school.
Nobody can really tell you what to do not take anonymous interent poster, U.S. News, or any other random information to seriously in making this decision. This is your life, your money, and your legal career and people that know nothing about you, your situation, your likes, your dislikes cannot give you any solid advice as to which school to choose.
No matter what you decide whether you make it in this profession will be heavily dependent on you. The name of your school only takes you so far and at the end of the day whether you sink or swim in this profession is largely up to you. Good luck to you whatever you decide.