If a dealer did the diffs and transfer case - it's all but guaranteed they used non-synthetic fluids to refill. Toyota uses synthetic gear lubes in all the cases. So you're going to lose some mpg from that, but probably not a lot. Maybe 1mpg.
Do you have an lift, level kit, or aftermarket roof rack? Or even a bug deflector? All of those will hurt your highway mileage. GM did a pretty good study a while back that showed that a bug deflector alone will cost about 1mpg.
The common issue on the 5vz (your 3rd gen 4R) was the O2 sensors. They could essentially wear out, but you wouldn't know because the engine wouldn't identify them as having an issue. So over time they'd slowly cause a slight rich burn condition and fuel mileage would drop. I considered it sort of like preventative maintenance on my 1996. I changed them at 150 and 200k miles. Both times I had a noticeable bump up in fuel economy after.
Those are the big ones I can think of. I don't think I'm aware of any O2 sensor issues on the 5th gens though.
The wheel bearings usually start making a lot of nose is how you know they're bad. Not from anything mpg related. If they were causing excessive drag, they'd overheat and fail pretty fast. They don't have a lot of cooling ability and the thermal runaway happens pretty quick if something goes wrong that increases friction a lot.
The one thing that can cause excess drag and you may not notice is a seized brake caliper or parking brake. After you drive next time put your hand on the wheels. The brakes will probably be kinda hot, so don't burn yourself, but feel if you can for any one of the wheels being a lot hotter than the others. That would suggest a frozen brake caliper.
Could also be your driving - style or the nature of your driving. Lots of city driving of course is going to reduce mpg. Driving north of about 90mph really kills the mpg too. The next time you're on an open stretch of highway on flat ground, reset the mpg calculator and see what it gets at 65mph. For a stock 4Runner you should get around 21mpg.
Finally - double check that your tires are inflated properly.
Those are all the ideas I know of.
Good luck.