Well, I had a 99 expy and the wife drives an 03 expy now and it does towing duty. I would lean towards the 03 since it's newer, has ind. rear suspension, which makes the truck handle and drive much better and upgraded brakes. Both are Beefy trucks for sure.
I loved the 99 after i got some adj rancho shocks and got rid of the stock goodyear wranglers for some Michelin ltx tires - damn thing was built like a rock (excuse the expression). Never a rattle or problem - cloths seats never showed wear etc.... What I didn't like was the steering was a little light and it was a bit underpowered with the 5.4 2v and mpg was between 10-11mpg.
Now, the 03 - maybe since it's an early first year build is, IMO, not as well built (still built well), but all around is better (engineered). Under warranty I had it in for a window falling in the driver's door and there were some c-clips in the 4x4 that were changed under a TSB. MUCH better steering, brakes and the Independent rear allows folding seats to the floor plus handles incredibly better. Definately enough power in the 03 (added CAI) and mileage is 11 all local and 17 hwy.
Does the 4v Navi require premium fuel? That would kill it there for me. GL with the choice.