why do you want that much lift? wanting 3 inches but not really knowing much about lifting (which is ok) leads me to believe you are more interested in cosmetics than function (which is ok). you are probably planning bigger tires etc
there is a sticked thread that basically just lists all the commonly available lifts for purchase, but does not provide any significant info on how to make the decision that is best for you. people often refer to it rather than type out something helpful.
if you are staying onroad and mellow trails (meaning not crawling rocks or doing anything remotely challenging beyond just a dit road with some inclination) then spacers are fine. it wont fix the 'softness" of the suspension most people in here are irritated by (nose dive, highway wandering and rolling in corners). it is true that spacers can compromise some of the function of your suspension (limiting or exagerating travel which can cause problems) read this:
http://www.bilsteinus.com/fileadmin/user_upload/user_upload_us/pdfs/Bil_LevShks_WebArticle_01.pdf
will you be susceptible to the issues outlined above? probably not if you never go offroad. if you do go offroad there is a chance you will be straining the limits of the suspension
icon? coilovers? pretty much overkill unless you actively particpate in a lot of 4x4ing as a passion. doesn't sound like your gig to me. they come with high a high price tag and a lot of maintenance. you will have to know how to wrench on your vehicle or want to learn.
to me the most sensible thing is to lift and improve at the same time at a reasonable cost. the most popular method for people like me (and probably you) who want cosmetic improvement and some increased function is a combination of bilstein 5100 shocks all around and new springs or spacers in the rear.
the front 5100's are adjustable and will provide 0.85, 1.75 or 2.5 inches of lift. the rear 5100s dont provide any lift, but will improve the ride/handling and will be compatible with something that will give you lift in the back (springs or spacers). you could save some money by using stock shocks in the backs with new springs or spacers.
if i was you i'd go new bilsteins all around, at 2.5 in the front with your stock springs, and get 2 inch lifting springs for the back with blisteins. all this stuff is available at
4Runner 10 & Up
conventional wisdom is that at 3 inches you need new upper control arms (UCA's) in order to be able to get within alignment specs. this mostly has to do with castor. castor is like trail on a bike, if you don't have enough castor the vehicle may drive like you have to constantly correct it at higher speeds like on the highway. more castor makes it feel a bit more stable.
i just wanted a mild lift. i don't do any chanllenging offroad stuff, and i don't have 33 inch tires to fill up the wheel wells. i have to cross the occasional snowy ditch, and do access some remote(ish) areas for fishing and camping. i went with 1.75 lift on the front and 1.5 inches on the back with spacers and new shocks. if i went any higher i think it would look goofy with the stock tire size. i might go up to 275's and some point. i also use 1.25 inch spidertrax spacers for a wider stance.