I have a MS in bioinformatics so I know a little about the bioinformatics landscape...
BINF is a really new field and there isn't any real rigid criteria and/or standards. Also, bioinformatics and computational biology are very similar and often the same thing with different names at different schools....hopefully in the future academia will adopt one name.
Anyway, because of how new it is there really isn't a set "ranking" and profs/students in the field just have differing opinions on the strengths of various programs.
1. Georgia Tech has the oldest BINF PhD program in the US. However, it's competitiveness depends on which "home school" you apply to. You can get a BINF degree from school of biology, school of biomedical engineering, cs, etc...
2. UCSF is pretty well regarded and competitive
3. Princeton has a program called "quantitative and computational biology"
4. CMU has a computational biology program that is housed in their cs department, which is ranked 1 in the nation. Because of this, it has high potential for reputation and growth
5. There are a lot of others...but again, no one really know their relative competitiveness