That might be the issue. You are using a rack not designed for a 4runner. Aerodynamics may be a part of it, lack of a foil in the front or not positioned properly might be part of it. A sunroof deflector might complicate things as it will deflect the air around the sunroof but might force it into the rack or they might just not work together.
I would take the rack off and see what happens. If the wind turbulence goes away then you have found your issue. If so then you have a decision to make, a functioning sunroof, a rack that may not be right for your 4runner, or just take it off when you're not using it.
Good luck.