Also, the airlines don't really care who you instruct for. Maybe with two identical candidates they might prefer the university CFI, but there are rarely totally identically qualified candidates.
What the airlines will care about is 1) your total flight time, 2) the quality of your flight time, and 3) that you don't get yourself into any trouble with the FAA for flying poorly maintained un-airworthy aircraft.
If the FBO is going to give you more flight time, a chance at getting multi time, and other quality types of flight time, and is not a shady place doing illegal things, then go for the FBO.