it depends on your preference. some like v-sync but some others not. for me the advantage of v-sync is to eliminate screen tearing. but for games that can't get 60fps using v-sync will result in lower frame rates. normally i will choose v-sync over frame rate (for cases where the games can't get 60fps) but if enabling v-sync will let the fps dip below 20 fps i will disabled it.
btw normally people will only use v-sync from the control panel when the in game option is broken or lack one (which is rare for most modern game). for me sometimes it depends on the game. for example in dead space series using in game v-sync will cap the FPS to 30 but if you do it from nvidia control panel it it will cap the FPS at 60.