Maybe you'll get some help here: https://goo.gl/OhlGBM

Scroll all the way down ;)

1) which school offered the most money?

2) which school has instructors whose work best aligns with your interests?

3) which school has the best cross registration opportunity?

4) which school has the best alumni connections in the firms/sectors you'd most like to work?

I don't mean to be a dick but if you're an M.Arch II and you cannot answer questions 2-4, then you should save both time and money, and not get the degree.  

I have got good funding from Yale followed by Cornell.I have applied to these universities,because I found the program seemed to be a tailor made one for me in various aspects.But now,what put me in this fix is,

1.the way they go about the course,

2.how does the program prepare the individual for practise, 

3.learning atmosphere amongst the students and the kind of students I should expect there

4. opportunities after graduation,

5.NAAB accreditation (how does it affect)

If anyone can give me inputs on any of these,It will be of great help. 

^ #5... oh boy.

What you have done is applied to two post-professional degrees, and one professional degree. I like the east coast schools better in general, but there is a pretty sizable issue.... they are not accredited degrees, so you can't get licensed based on them.

I think a real big question here is if you have an accredited undergraduate degree? If not, and you want to go into practice, why would you even apply to post-professional degrees? If so, then Yale seems like the more obvious choice, because having two accredited degrees is not of any extra benefit.

For #5

You cannot get accreditation for AIA with M.Arch II degree (unless you have NAAB accredited B.Arch or M.Arch).

You have to apply separately. There is no program that provide you with accreditation if you are from M Arch II

yale's MArch II is really great. you'll have opportunity to travel and learn from excellent visiting practitioners. New Haven is more connected to NYC then Cornell

If you have aid from Cornell and from Yale then you should not consider SCI-Arc. My concern about SCI-Arc is that they are becoming a pay to play school. They have more then doubled tuition in under a hand full of years to put them inline with Ivy League school's - yet offer substantially less in aid. Beyond their advertisements about 3 specific regional scholarships, one for a LAUSD student, one for a Mexican student and one for a European student - they provide much less funding and no funding for any studio trips etc... certainly not in the way the Ivy's do. Even more concerning is they have a tendency to give scholarships to already wealthy millionaire students - which appears to be in some hope of donations. SCI-Arc is an extraordinary place but in my opinion their focus on wealthy students is beginning to hurt their diversity. There is a lot of talk about wealthy students at the school to donating money in order for the school to give them a "Merit Scholarship" as resume boosters... I am not sure if that is the reality but it is a reality that many wealthy students are given substantial scholarships and awards for many times mediocre work. I am concerned every aspect of the school is becoming purely financial and purely about how much money you can spend to pay people to assist you in your studio work (This I can say is true that it is very common in the school for wealthy students to have paid people doing their studio and thesis work for them, writing their cultural study essays and the school turns a blind eye and to many extents encourages and rewards it).

Thank you all for your advice :)