I hope someone responds because I ran into the exact same issue this past weekend. I was able to get the fender flare loose enough to move it out of the way without completely removing it, but I got stuck on the plastic plugs that hold the wheel-well lining in place. I'm afraid I'm going to break them or tear the liner trying to pry them out.

2001 Silver 4Runner, Nokians, Thule rack
2003 Red Tacoma Extended Cab, V6, 5-spd