I've owned a 98 sr5 and now my 06 ltd so I figured I'd weigh in...
Reliability: Both are very reliable, i wouldnt say that one is more reliable than the other. Each gen has some "known issues" or "common problems" that will happen or are more likely to happen but I wouldnt choose one over the other for this category.
Ruggedness: What are you planning on doing to it after purchase? A stock 3rd gen feels more rugged than a stock 4th gen. It definitely has more clearance and you can find 3rd gens with rear lockers and I think ive even seen some with center and rear lockers. The 4th gen can be found with a center or a rear locker as well. Lockers = more offroad capability = ruggedness.
If you want the most rugged without modifications, I'd go with the 3rd gen. A stock 3rd gen definitely looks and feels more like a truck than a stock 4th gen. I also liked thy physical 4wd shifter on the 3rd over the electronic switch on the 4th.
Fuel Economy: Negligible. I got similar MPG between my 98 and 06 but its hard to compare due to the different mods on each. The 4th gen does have more power and can hold about 5 more gallons so you can go longer between fill ups but it will also cost more to fill a 4th gen.
In the end, its what you're looking for. If it's ruggedness and you do not want to mod it, go with the 3rd gen. If you do want to mod it, how much you want to spend is the factor. The cost of modding is fairly the same across both gens but the up front cost is clearly cheaper for a 3rd gen.
if up-front cost isnt a concern, go with whatever you feel more comfortable sitting in and what looks better to you. You can build either gen as a highly capable off-road vehicle. If you're not going to mod it and you want ruggedness, go 3rd gen.
You can eliminate reliability and fuel economy from the mix as both gens are close enough when comparing the v6.
if you are going to mod, I'd suggest taking a look around at build threads to see what people commonly do to each gen and deciding which you like better that way. It may come down to the smallest of features (ie 98s and older have awful cupholders, 99+ has better and the 4th gen has the best IMO).
Think about what you want to do with it, what you want it to look/feel like and how much you want to spend. Once you do that you'll be able to look at rigs on this site to determine which gen meets your desires the most.