Seattle, WA, offers top salaries for Principal Scientists, averaging around $192,250 annually. San Francisco, CA, closely follows with an average salary of $191,209. Job seekers in these cities can expect competitive compensation packages in this field. In Boston, MA, and San Diego, CA, salaries for Principal Scientists average around $175,169 and $165,301, respectively, providing attractive opportunities for professionals. Indianapolis, IN, rounds out the list with an average salary of about $142,161 for Principal Scientists.