Re: 89' Strat or 99' Strat...
I think it's going to come down to which one you prefer. Which one feels and sounds the best. As far as I know, the pickups on a standard American series will be pretty much the same. It's the Deluxe models that offer Vintage Noiseless, SCN, or other options.
The only thing I could recommend to be on the lookout for is the infamous "swimming pool route" where they cut corners by routing one giant hole under the pickguard to accommodate all pickup configurations. Later models are routed either specifically SSS, HSS or HSH. The '89 may be routed this way. Whether or not that's a bad thing though is debatable. Some people swear they hear a difference in sustain, others prefer it and think of it as a soundhole. Dunno. Again, I really think it'll come down to which offers YOU the most mojo.