Yeah, finding apartments online is tough. There are nice and not-so-nice areas in both G'town and PI. For someone not familiar with the area, I'd suggest starting in PI, but G'town is also a neat little town if you can find the right place.
I've included a couple links below that may not have popped up in your search. The first one is for classified rental ads in the PI newspaper. Several of the larger RE companies have ads listed in this section, so you may want to give them a call, also. I noticed there are quite a few listings for rentals in TrueBlue condos. Those are very nice if you can get them to negotiate the price down a little.
Coastal Observer - Classified Ads
Lowcountry Real Estate, Rentals and Commercial | Charleston, SC | Classifieds (search zip code 29585 for PI, 29440 for G'town)
If you have questions about specific locations, just post 'em back on here and somebody will be glad to help. Good luck!