I've recently purchased a 99 4runner and I can confirm that the stock speakers are the worst ! it did have a crappy old Sony cd player that the previous owner had placed with the stock tape player.
I've just bought a JVC cd/mp3 player and 2 pairs of Alpine speakers
Alpine SPR-136A 5 1/4" R-Series Component 2-Way Speaker
Alpine SPR-174A 6 1/2" Type-R Coaxial 2-Way Speaker
JVC KD-S890 CD/CD-R/CD-RW/MP3 Receiver
for about $400 shipped but have not installed them yet.
Sade