The 4th Gen 4Runner produced for the North American market does not utilize a traditional Vacuum Assisted Brake Booster. It utilizes a Hydraulically Assisted Master Cylinder Unit that has an electric pump to pressurize a nitrogen filled accumulator pod to provide assistive force. This system provides a relatively input pressure vs. pedal travel and leads to many people mistakenly believing the system to have a "soft" or "spongey" brake feel. The reality is that the system provides a very consistent pedal stroke with minimal input force variation (i.e. instead of the pedal pressure increasing as you get further to the floor, you can easily push the pedal all the way to the floor with very little increase in over all pressure applied.)
The braking system is designed to be this "easy to operate", but it is a very different feeling than typical vehicles (even some Toyotas that have a different version of the same hydraulically assisted system since they tend to tuned differently), it takes some getting used to. It's very common to under apply the brakes (particularly in the V8's when the A/C is on) and have them "creep" because the pedal pressure is so consistent you can let up a little and not notice right away the brakes aren't "biting" anymore. There's other factors that can add to this such as glazed pads/rotors, seized/seizing calipers, ect. I know my 4Runner's brakes are a bit glazed and don't bite as well as I would like (will rectify that eventually one way or another.)
Bottom line, it's probably normal due to the way the braking system is designed and the low-end torque of the 2UZ-FE in an off-idle situation (i.e. A/C running) if you let off the pedal slightly. There's also the possibility that the brakes are not gripping well enough due to glazing and/or caliper issues; so it doesn't hurt to give them a look anyways.