from what i understand, pi's are considered a category of their own in terms of letter of recommendations...they would fall under the "miscellaneous" category that some schools give you the option to fulfill. but out of the two (science professor and employer) they are much closer to employer
just b/c hes also a professor doesnt mean u can use him as one of ur letters to fulfill the "science professor" requirement. u have to actually have taken his class, and the letter in that case should be focusing on you as a student, not you as a research assistant, although that could still be brought up as complementary material