Amazon.com. In my opinion, Kenwoods are the best value. I have Alpine Type S speakers and Kenwood speakers and like the Kenwood's better. They're typically cheaper. Alpine Type R's should be amp'd which would be another 200$ or so for that, so stick with Kenwood's. Get components because you can mount the tweeter wherever you want. Amazon has everything much cheaper than BestBuy and Crutchfield. Crutchfield is nice because they give you brackets, which makes installation much easier. But you can usually find those in other places on the internet.
So to answer your question, in my opinion it is best to order Kenwood speakers from Amazon, and buy mounting brackets from some other online store and install everything yourself, it's really easy and will save you alot of money.
Now you need a Head Unit. They do allow you to crank it up louder and the sound is much clearer than the stock one. If you need help regarding HU's let us know whether you want a touchscreen style ( Double Din ), or a basic stereo. (single). I'd get it from Amazon once again, but check Crutchfield first because that will tell you whether it's 4Runner compatible. But I wouldn't buy it from Crutchfield, just get the mounting bracket and wiring harness from them.
Prices would be:
80-600$ for head unit depending on features and brand
30$ for mounting bracket
5$ for wiring harness
Subs- Anything non- Sony will sound great. Just buy the best you can for your budget. Read reviews off Crutchfield. Don't go by the peak power rating. Go by the RMS, that is how much continuous power is going to them. Peak would be one huge blast of bass, which is important, but RMS is by far the more important statistic.
Amp- Just get an amp that can power the RMS of the subs. Alpine and RF are some of the best amps but very pricey. You are probably better off with a cheaper brand, but don't go so cheap that you are buying an unreliable product, for example, Lanzar. Their stat's are over-exaggerated. Get a wiring kit from Amazon. As far as I know, they're all the same.
As you can see, it's hard not to spend a fortune on car audio. It's one of the biggest scams there is in my opinion because they are marked up beyond belief.. It's up there with razor blades, movie popcorn, soda, Advil, whey protein, and professional sports jerseys. So be prepared to spend a lot of dough.