Whichever truck you like better is the one you should buy, i would try to get the 97 for a little cheaper. Coming from someone with almost all the 99+ stuff on his truck, it really doesn't matter much, i did the center and roof console swaps, 99+ headlights, 01 tails, and guess what, i still use my dash cupholders because i just leave my phone and wallet in the regular console cupholders, and i haven't used the sunglasses case in the roof console in months, the 01 tails on the other hand are sweet, but that 99 won't have them anyway.
Everyone will be like OMG 99 the best year and the HOLY GRAIL of the 4runner, but its really no different then the rest of the years, yes they had taller springs when the left the factory (on some models), but its been nearly 14 years since they were new, those springs have got to be shot by now and sagging to the same height as the rest of the 4runners.