Capturing works in non-HQ mode, it means you may capture only non-HQ object.
It is more intresting than capturing whole system at once and availability always to have starting point for faction representatives.
NY HQ List:
Baltimore Shipyard - Deep Space Engineering HQ
Battleship Missouri - Liberty Navy HQ
Buffalo - Liberty Rogues HQ
Detroit Munitions - Ageira HQ
Fort Bush - Liberty Police, Inc. HQ
Newark Station - Interspace Commerce HQ
Trenton Outpost - Universal Shipping HQ
I've did the list of HQ long time ago so at NY seems to be you may capture only Rochester - but try, maybe others works too, if not - tell me.
Think i have missed something with HQs so you may tell me which base must be of aporpriate faction HQ and why.