I have a 2005 V6 SR5 4x4, and it has six fittings. There are three of them on each propeller shaft. {Of course, the 4x2 models will only have three fittings on the single shaft.}
***From everything I have read, the 2wd models do not come with grease fittings in the drive shaft.***
It is kind of hard to describe how to get to them, but you will have to use a flexible-tip grease gun. You should pump in enough grease so that you can see it squeeze out on the other side of the zerk. The first time will require a little more effort than will subsequent tries, as there will be little grease from the factory.
***When it comes to the slip joint in the rear shaft, it isn't a good idea to pump grease in it until it comes out somewhere. Because the slip joint is designed to slide in and out to accomodate the rear suspension movement, filling the cavity inside the joint can cause the joint to not compress when it needs to. The shock to the two ends (transfer case and differential) when the joint does not compress could cause damage to them. Toyota recommends removing the drive shaft, and dissasembling the slip joint to remove old grease and clean it if necessary.***
Use a good synthetic grease for all the fittings, and that way you don't have to worry about which type is for what fitting. It will only cost pennies more each use, and the peace of mind will be well worth the $4 or $5 for a whole tube of the good stuff!
You will easily see two of the zerks on each shaft, but the third one will be obscured a bit at the point where it resembles a U-joint. Trust me - it is there.
Good luck to you with your 4Runner! You chose a great vehicle.