Re: Replacing stock suspension
Suggestion: replace the 4 shocks, and see if that resolves the ride quality issues you are experiencing. Note that if the springs have not sagged, they still should be good.
If no plan to lift, Bilstein 4600s are the best bet.
Bilstein 5100s are the same as the 4600s, on the inside, but have the ability to be adjusted up/down (for instance, to deal with a small amount of spring sag at the front). Note, though, that the 5100s are only zinc coated (shiny when new, looks like crud after a few winters), and the 4600s are painted (hold up much longer, in the appearance department).
I wouldn't bother with any other brand of shock, as Bilsteins are demonstrably the best (their unique internal structure provides a better compromise than others can do, and is why they cost a bit more), and the ones Toyota chose for all of the special editions, because of it.
Note that if there is noise from your suspension while going over bumps you could have a perished bushing somewhere. A good mechanic can find it on a hoist by prying with a long pry bar and watching for undue movement. Also, a poorly adjusted parking brake internal mechanism can make a hell of an annoying rattle on bumps.
After changing shocks, it is a good idea to get the alignment checked. Make sure that they lube your eccentric bolts on the lower control arms when they do it so they don't seize over time (worst case requires new lower control arms after cutting the seized bolts off).