I got my private, instrument, commercial, CFI, and CFII at FBOs where the instructors were freelance. I've also got about 1400 hours as a freelance instructor.
Shop around and pick your instructor carefully, but there are plenty of good CFIs working for Mom and Pop operations. They just don't have the resources and standardization training of larger schools.
There is no difference in the license you get from a FAR 61 school, but there may be a difference in the training you get.