The window is most likely off the track. With the back window up, take off the cover by lifting it up. Then unscrew 6 or 8 screws from the metal cover. Now remove the plastic overlay. This will allow access to the back window motor and window. There are two sliders witch the back window sits upon. If the window is off of it's track it will not go up or down or will have a hard time doing so. Also make sure that all the electrical connections are on at the back motor. If this doesn't work try a possible blown fuse? Hope this helps.
The 2004 Toyota 4Runner has 57.2 in. of rear shoulder room.
The 2003 Toyota 4Runner has 34.7 in. of rear leg room.
The 2007 Toyota 4Runner has 34.6 in. of rear leg room.
The 2004 Toyota 4Runner has 55.3 in. of rear hip room.
The 2003 Toyota 4Runner has 57.2 in. of rear shoulder room.
The 2014 Toyota 4Runner has 32.9 in. of rear leg room.
The 2009 Toyota 4Runner has 34.6 in. of rear leg room.
The 2003 Toyota 4Runner has 39.1 in. of rear head room.
The 2012 Toyota 4Runner has 38.6 in. of rear head room.
The 2007 Toyota 4Runner has 39.1 in. of rear head room.
The 2011 Toyota 4Runner has 38.6 in. of rear head room.
The 2014 Toyota 4Runner has 55.7 in. of rear hip room.