It's definitely better. How much? That's debatable. Most people do the Tundra brake upgrade when they are already in need of new brakes so going from bad brakes to good brakes is already going to produce a noticeable difference. Without going from good 4Runner brakes to good Tundra brakes it may be difficult to really tell. I think you will notice it most when/if you do any towing.
I plan to do the Tundra upgrade next year, mostly because it seems as though the 4Runner rotors are easily warped.