http://www.footballoutsiders.com/stats/fplus
Central Florida is 51st, Nevada is 52nd and Utah State is 53rd - all above average teams (with the median being 64).
PLus, I did mention there were 11 teams ahead of us that were FCS schools in Pomeroy's rankings but since I want to compare apples to apples, I limited the comparison to just FBS programs.
You are right that there are a handful of good FCS basketball programs - but just a handful. About the same number of schools as the number of FBS schools with really bad basketball programs. So it evens out in the end.