I always find these ratings interesting (if not dispositive) because they take away some of the biases of past history and reputation that keeps teams like Montana way up in the ratings despite records, play and strength of schedule.
Sagarin-USA Today Ratings have the Big Sky Conference as the top FCS Conference.
http://www.usatoday.com/sports/sagarin/fbt10.htm
Big Sky Conference
59 Northern Arizona
77 Montana State
78 Eastern Washington
99 Montana
105 Sacramento State
119 Portland State
142 Weber State
184 Northern Colorado
204 Idaho State
Massey Ratings (first number is overall combined with FCS and FBS teams; second number is FCS alone)
http://www.masseyratings.com/rate.php?lg=cf
92 Northern Arizona 3
95 Eastern Washington 5
109 Montana State 11
111 Montana 13
142 Sacramento State 23
156 Portland State 30
159 Weber State 31
213 Northern Colorado 54
267 Idaho State 78
Sagarin-USA Today Ratings have the Big Sky Conference as the top FCS Conference.
http://www.usatoday.com/sports/sagarin/fbt10.htm
Big Sky Conference
59 Northern Arizona
77 Montana State
78 Eastern Washington
99 Montana
105 Sacramento State
119 Portland State
142 Weber State
184 Northern Colorado
204 Idaho State
Massey Ratings (first number is overall combined with FCS and FBS teams; second number is FCS alone)
http://www.masseyratings.com/rate.php?lg=cf
92 Northern Arizona 3
95 Eastern Washington 5
109 Montana State 11
111 Montana 13
142 Sacramento State 23
156 Portland State 30
159 Weber State 31
213 Northern Colorado 54
267 Idaho State 78