Both I guess...
What is your purpose for the truck because everything key is improved on the later trucks. You will either pay up front now or pay later with mods and having to fix it. You either need to save more and get what works or look at something cheaper that fits your needs.
Are you planning to race...? 99/00 is about .5 slower than the 01+ models...
Are you planning to mod...? 99/00 will cost you more to go slower...
Towing...? The 99/00 isn't rated as high as the later models...
Heads, intercooler blower, driveshaft, gears, etc. are all better on the 01+...