Oh come on, everybody can churn out papers and patent filings.

If you go by Nobel prizes, the ranking is different (leaving out non-US contestants):

Physics:

1. MIT

2. Harvard

3. Berkeley

4. Chicago

5. Columbia

Chemistry:

1. Harvard

2. Berkeley

3. Chicago

4. Caltech

5. MIT

Medicine:

1. Harvard

2. Rockefeller

3. Columbia

4. Caltech

5. WashU

Conclusion: Stanford is overrated.