The GT 540m will perform significantly better.
The Intel HD 4000 is basically equivalent to a desktop GT 520 graphic card while the mobile GT 540m would be roughly close to the GT 440 graphic card.
Playing Crysis with the Intel HD 4000 would give you somewhat acceptable performance in the mid / upper 20's FPS with low quality graphic settings on a laptop with a 1366x768 resolution screen. The GT 540m should be able to provide roughly low 30's FPS using medium quality graphics with the same resolution.