Here are two top candidates:
UTEP’s all-time low score of 17 pts at the 1981 NCAA XC Championship meet (when 23 teams competed) was done with this team:
1 Mathews Motshwarateu (age 23, Botswana)
2 Michael Musyoki (age 25, Kenya)
3 Gabriel Kaman (age 24, Kenya)
5 Suleiman Nyambui (age 28, Tanzania)
6 Gidamis Shahanga (age 24, Tanzania)
Two of these runners would be above today's NCAA D1 age limit of 24.
Stanford produced the next lowest scoring team with 24 pts at the 2003 NCAA XC Championship (when 31 teams competed) with this team:
2 Ryan Hall (age 21, Big Bear Lake, CA)
3 Grant Robison (age ??, San Angelo, TX)
4 Ian Dobson (age 21, Klamath Falls, OR)
5 Louis Luchini (age 22, Ellsworth, ME)
10 Adam Tenforde (age ??, Richland, WA)
Coach Gerard was named the 2003 NCAA Men's Cross Country Coach of the Year after this Stanford victory. "To be honest, I prefer that it be 'Manager of the Year'. I've really just managed these athletes. It was really assembled and developed by Vin Lananna (former Stanford Director of Cross Country/Track & Field) and Michael Reilly (former Stanford assistant coach). I have to give them credit where credit is due."
A third candidate might be Arkansas which scored 31 pts at '93 Nats where 22 teams competed. This was coach John McDonnell's 4th consecutive NCAA XC championship. Only other school to win 4 consecutive NCAA championships was UTEP (1978-81).
FYI, Drake scored 25pts at 1944 Nats, but only 6 teams competed that year. And Michigan State scored 28 pts at 1956 Nats but only 14 teams competed. Yes, I know there are measures other than Nats Point Score(NPS) to guage how great an XC team was, but NPS is a very good measure.