How does one define a top program? History/tradition, recruiting success and recruiting base, recent success? I would argue that despite MSU's recent success that they still aren't a top 15 program.
I would say in no particular order I would put these teams above MSU:
Alabama
LSU
OSU
Michigan
Auburn
USC
Texas
Oklahoma
Florida
Florida State
Clemson
Notre Dame
Georgia
Penn State
Miami
I go by right now really when I consider top programs. I try not to set too many parameters.
I would say Michigan State is a better program right now than the Florida, Miami, tied with Notre Dame. I think USC frauded people with an NFL QB, and at best will be 9-3/8-4 for a while. I'd take out Texas and Michigan, put in Okie State, and could see Washington or Stanford make a case.
Now, if you want to talk all time programs, no MSU is not one. Probably not a top 25 all time either.