What are the best Universities in the Northeast for Computer Science/Engineering?

MIT and Yale

The best in the northeast for engineering are, in this order (best on down):

MIT
Cornell
Carnegie Mellon
The Cooper Union
Princeton
Johns Hopkins
US Military Academy (West Point)
US Naval Academy (Annapolis)
Penn State University Park
Bucknell
Columbia
Rensselaer Polytechnic
U Maryland College Park

There are a ton of other good schools as well, but these are the best of the best. Not all of those offer computer science, though - some just engineering.

The best computer science schools are:

MIT
Carnegie Mellon
Cornell
Princeton
U Maryland College Park
Columbia
Harvard
Brown
UMass Amherst (which also has a top 50 ranked engineering program, but wasn't ranked quite high enough to make my above list)
Penn
Yale
Johns Hopkins
Penn State