This is a tough question to answer, mainly because there are too many ways in which to characterize qualitative distinctions between programs, and almost all of them are not accurate portrayals of the quality of graduate study there. Oh, and I'm not going to worry about applied because I'm not sure that I very much care. And I'm basing my commentary on the format of your own post.
Stanford - (Ravi Vakil http://math.stanford.edu/~vakil/
)... okay, well Stanford is good for AG, but not on the basis of a single individual. If we're going down that road, though...
Columbia- Perhaps the world's most influential group on higher AG; and, of course, Aise Johan De Jong!
Princeton- if you care about arithmetic AG, this is Mecca
Michigan- A number of great algebraic geometers work here, too many to list
UIC- It seems that most people who study here study AG
UTexas- AG is a major research area here...
Utah- ...and here.
Miami- Yes, Miami! And Maxim Kontsevich, fields medalist, who works on algebraic stacks.
I'll just list the best ones: Harvard, Michigan, Princeton, Wisconsin, UMN, Berkeley, and UCLA.
UCLA -(Terrance Tao)- yes, of course!
UCSD - (Harold Stark)- Mhmm
UIUC - Bruce Berndt- again, fair...
PRINCETON!!!! - And not just for the presence of Andrew Wiles...
Yale - A lot of the professors there do representation theory. -a silly reason to pick out Yale for RT, though it isn't entirely untrue.
Harvard- some of the most important work in RT has come from this bunch in the past few decades; individuals like Gaitsgory do incredible work here.
Princeton- a lot of work is being done here on the langlands correspondence... fruitful work. It's probably the top RT school right now.
Harvard- Michael Hopkins, Jake Lurie
Stony Brook- Milnor!!
UChicago- Peter May et al.
UPenn- Specifically algebraic topology
Berkeley- Again, the algebraic kind.