I edited my post because NDSU has 92 wins not 90 in this decade. Which is insane. It also means that NDSU "only" needs to average 9 wins a season to tie Montana's record.
Best decades by teams currently in FCS:
Decade Team Wins 1890's Pennsylvania 124 2000's Montana 119 1890's Yale 116 1890's Princeton 108 1980's North Dakota State 103 1990's Youngstown State 103 1890's Harvard 103 1900's Pennsylvania 100 1900's Yale 100 1980's Dayton 99 1980's Eastern Kentucky 97 1970's Grambling State 96 1980's Furman 95 1970's Delaware 94 1990's Northern Colorado 93 1990's Montana 93 2000's North Dakota 93 2010's North Dakota State 92 1990's Dayton 92 1980's Central Arkansas 91 1900's Harvard 91
Ivy League teams could schedule as many games as they wanted way back when. For example: http://www.bisonville.com/fanguide/1892/team000586.html