Oh, I thought you were talking about Colony Island since the subway passes over it. Even so, I still by what I said for this reason: size doesn't matter, but practicality does. I assume Colony Island is supposed to be Liberty City's equivalent of Roosevelt Island, a small, residential island underneath the Queensborough Bridge, located between Manhattan and Queens. Charge Island would then be the equivalent of Ward's Island, a mostly *uninhabited* island located slightly north of Roosevelt Island. Since I'd assume that R* is going to try to keep the two islands close to their real-life counterparts, there wouldn't be much point in having a station at Charge Island, since there would be nothing but parkland, bridge supports, and possibly some public facilities (mental ward), if they wanted to make it really true to life. Colony Island would be a better choice as it'd actually offer some incentive for using the station, in that it allows you to access a "mini-village" in the city.
Hopefully that wasn't too convoluted.