are you looking to replace the whole set or piece ba piece lang?
it depends on your taste, your music, and your budget.
first, what sort of sound are you looking for in your strat? the stock alnico pickups on the reissues are pretty good already. if you want a bright, jangly strat tone, get vintage spec pickups. if you want a round fat, glassy, bluesy tone, get a hot or overwound set. if you want a modern-sounding strat, get EMG's.
next, your music. that kind of music will you be playing with that strat? kasi the tone you'll be getting might not match the particular music you'll be playing. like a low-output vintage set might not do justice to heavy metal music, you'll just end up frustrated.
last, budget. if the budget is limited, the choices are limited, if you have a pretty high ceiling on your price, the possibilities are endless. there are the cheaper GFS pickups (which are good na rin) then there are the mid-priced dimarzios and duncans and fender CS pickups, then there are the boutique ones, the lollars, fralins, bareknuckles, etc.
so yun, think of what you want muna para you won't end up spending on something na hindi mo magugustuhan in the end. good luck!