Look, you're old enough to decide what's right/wrong and evaluate the consequences for yourself. You say you're parents don't want mods, but you do. It's not my place to tell you to listen to your parents; you and your folks can sort that one out.
You came here for mod suggestions. Looks like you avoided the classic "do a search" response (probably because everyone had more fun advising you on purchasing your own car and respecting your parents). Which is all good, I would suggest taking much of the advice given here to thought (truck related or not), having your own car that you bought is pretty satisfying.
However; I won't judge. My first car was bought by my parents, I spent some money modding it (all cosmetic), sometimes they agreed, other times they didn't. Flash forward, now I've bought my own car, and have done my own mods, and I (and I'm sure they) like it better that way. You'll get there.
Others say "go have fun." Well for a lot of us, this is the fun (isn't that why we're on a common interest forum?). If you prefer spending your friday and saturday nights in the dash and underneath your 4runner, by all means, enjoy it.
But I digress, you wanted mod advice:
For now, I'd go with the previously mentioned "Easy Weekend Mods" Thread for little ideas. On my first vehicle I was partial to auxiliary lighting. Cheap auxiliary reverse lights can be had for under $50 and can make a world of difference when backing up at night, and give you an introduction to tapping wires and mounting equipment to the vehicle (often they are easy to mount, sometimes they even just use fat zip ties for your hitch or something). The fog-light anytime on mod is a nice quick one too, probably even easier than adding reverse lights. I picture my 16 y.o. self loving the ability to run fog-lights without headlights on (illegal in some places from what I hear, but hey, it looks cool right?) Browse that Build Thread Directory, even heavily modded vehicles probably got started with a tiny mod here and a little one there (it's not called catching the bug for no reason), so they could have some cool things you might like, such as plastidipped logos, or upgraded speakers.
Take care of your truck (don't forget about maintenance! oil changes, brake changes, fluid checks, all important things that you can't allow yourself to lose track of while being in full mod-mode!), learn about it, have fun doing it, mod it, be nice to your parents, then argue with them, then be nice again, then do that a few hundred more times and by that time you may be old enough to buy your own car, always respect your parents, accept consequences for your actions (good and bad), and be grateful you drive a 4Runner.
/end Devil on the shoulder/'cool uncle' rant
edit: non-noticeable? You could always just start replacing OEM things that need it. You get to work on your car, you make it ride better, you learn about it, and you can tell your parents you're making it safer, it's a win-win across the board. There are bushings and such that maybe need replacing at almost 9 years old and some aren't too expensive. Maybe new poly swaybar bushings?