FISA does not trump the Fourth Amendment. Moreover, this controversy is about tracking the location of Americans in America, which is beyond the purview of FISA.
I don't think it is irrelevant at all. The problem though is that the court actually ruled officially in Jones on very narrow grounds which are inapplicable here. That 5 justices went further and said that general surveillance could reach 4th Amendment problems if large enough in scale, and that this would require rethinking existing precedent throws a real monkey wrench in things but it is premature to say the Supreme Court has ruled on this issue.
http://en.wikipedia.org/wiki/Foreign_Intelligence_Surveillan...
http://en.wikipedia.org/wiki/Foreign_Intelligence_Surveillan...