What are the best colleges that focus on historical linguistics for undergrads?
That is really specialized. You might want to start by identifying institutions with strong graduate programs, and then check to see what the undergrad offerings are.
This depends a great deal on your languages of interest and your stats. Tulane is a powerhouse in Mesoamerican linguistics, for example, whereas Chicago and Johns Hopkins are the primary options for comparative Semitics.
The top schools for Indo-European linguistics are Harvard, UCLA, and Cornell, but there’s many other good options (Berkeley, Chicago, Michigan, etc.).