Since you're planning to get the SE, this model comes standard with the xreas system. This means that your lift options will be limited to one type of lift suspension: spacer technology.
Daystar Suspension
Revtek Suspsension
Nitrous Enterprises
My personal recommendation is to get a maximum of a 3 - 3.5 (if you really want to push it) lift. I don't recommend running anything more than that. With this lift, you'll be able to fit larger tires (depending on model and type of course).
Installation is not an easy task for the xreas but any person that is mechanically skilled will be able to install it with ease. If you want to install it right as soon as you get your 4runner, you're free to do this.
Good luck