Jason,
First off, you're gonna take a big hit when trading in your '02 4runner. A very big hit!
GS300...my brother has a '99 model. GS300 is damn reliable...in fact, it is the most reliable car in it's class, by far! It is solid. Good crash test results. Very nice (but dated when compared to ES300) interior. Quiet, comfy ride (very little wind noise). Cupholders are tiny (again, compared to newer Lexuses). Performance is average at best...0-60 in about 7.8 seconds. Braking is average (GS430 has better braking). Handling is average. It is more of a comfortable highway cruiser than a sports car.
There will be a new GS model out in late 2004 (as 2005 model). That's a good and a bad thing. If you plan on keeping your GS300 for a LONG time, then you should get it now because you can get GREAT deals on it. However, once the '05 model comes out, your resale value will drop big time! (Similar to what is happening to your '02 4runner because the '03 just came out.) Again, if you plan to keep the GS for a long time, then resale value should not mean much.
If you buy a GS now, MAKE SURE YOU GET A GOOD DEAL with good financing rate. I am pretty sure you can get one close to invoice.
BTW, the Mark Levinson system in the GS is a MUST HAVE! That system sounds REALLY good! It kicks the crap out of my M3's Harmon Kardon system.

Another good option to get is the DVD navigation system. Wood steering wheel is always nice to touch!
If Lexus is not going to give you a great deal on the GS300, then i would look elsewhere. For example, for the price of GS300, you can get a fully loaded 2004 ES330 (NOT ES300). With the ES330, you get a faster car (3.3L V6, same as in the new RX330, Sienna, etc.) with slightly more room than GS300. (HOWEVER, the 3.0L inline 6-cylinder in the GS300 is a great engine...some say superior to any V6!) ES330 won't be redesigned anytime soon...so it's resale value will be good for many more years. Handling probably favors GS300, but ES330 is good enough.
Have you considered the new Lexus RX330?? Again, for the price of a fully loaded GS300, you can get a pretty good RX330. Resale value will be good for many many years since it's just redesigned this year (as '04 model).
If you want to learn more about RX330, see this COMPARISON thread:
http://www.toyota-4runner.org/showthread.php?s=&threadid=147
And you will still stay in the SUV family!
Hope this helps.