I'd like to bump this more than 6 months later, because I found a program to disable VSync in Freelancer on ATI GPUs fully: It's name is RadeonPro: http://www.radeonpro.info/en-US/
Just create a profile for Freelancer, and force VSync Off in the Tweak panel. This way, your FPS won't be locked to 60 and you can enjoy Freelancer without Input Lag, even when Alt+Tabbing.