Some big differences:
1) GSIS is on the Peak while HKIS is soutside and quite a bit apart from each other. Having said that there are school buses everywhere so it should not be a huge deal as long as you are on the island.
2) GSIS population is more cosmopolitan while HKIS is more American. Some people like to be with their own kind while others like to experience different cultures.
3) GSIS has an excellent sports programme but a lot of their sports are international (eg: Field Hockey) while HKIS also has excellent sports but they are mostly American (eg: Baseball & Football).
4) GSIS has practically no religious classes other than world religion classes while HKIS is a Christian school founded by Christians and religious classes are mandatory.
5) GSIS is seen/deemed to be a lot more academic, harder, more homework and where more gifted/high achievers go. HKIS is seen/deemed to be a middle of the road school with excellent teachers and facilities.
If you are coming here for a short time, pick HKIS. Its as American as you're going to get your kid wont know the difference.
If you are coming here for longer term, you should consider things more carefully as neither school has a particularly great Chinese curriculum and both schools are mostly English only with very little emphasis on Chinese.