Ranking the best teams depends on the timeframe. From the “Point System for Nationals finishes” I created, below are the results for mostly 10 year periods (plus all-time at the end). The College Men’s Division started in 1984.

Here’s a link to the All-Time Top 10 College Teams on the Ultimate History website showing the details of where each team finished at Nationals each year and how many points each team received:
www.ultimatehistory.com/stats/team-all-time-rankings/ 

1984-1989 Men (only 6 yrs):
1. UCSB
2. Stanford
3. Cornell

1985-1994 Men:
1. UCSB
2. UNCW
3. Cornell
4. Stanford
5. Oregon

1990-1999 Men:
1. UCSB
2. UNCW
3. Carleton
3. Stanford
5. Cornell

1995-2004 Men:
1. UCSB
2. Carleton
3. Stanford
4. Colorado
5. Wisconsin
5. Brown

2000-2009 Men:
1. Wisconsin
1. Colorado
3. Carleton
4. Stanford
5. Brown

2005-2014 Men:
1. Wisconsin
2. Carleton
3. Colorado
4. Florida
5. Stanford

1984-2015 Men (all-time):
1. UCSB
2. Carleton
3. Stanford
4. Wisconsin
5. Colorado
6. Oregon
7. UNCW
8. Cornell
9. Brown
10. Florida