Have recently replaced my brake pads & discs on my bike as well removing my fork & greasing my headset bearings. Recently i have noticed that my fork is vibrating quite heavily under braking. I have sat with the front brake on & rocked the bike back & forward, the fork seems to be moving.

So am i correct in thinking its a headset problem as its the original one thats been on the bike for over 2 years

Most likely culprit is a loose headset,if not then fork bushes.

i can feel it through the bars when i rock it, think i may have to replace headset, was wanting a new one anyway

It's more likely to be whatever you've done to the brakes. Make sure that the headset is correctly preloaded and make sure that the new brake components are properly fitted (like rotor not back to front). If you have the old rotor and pads, it's a five minute job to see if the same vibration occurs with them back in use. If you have the same brake in the rear, try swapping the pads and see if the vibrations still occur.

rotor is on right way will try changing the pads, thanks

Twist your bars sideways. So as the front wheel is perpendicular to the frame. Then try rocking it back & forth again. If the movement is still there it just means your headset's loose. Means you've either re-assembled it wrong following the service or just not re-tightened it enough. Easiest thing to check first. So before you go off replacing it or doing any other convoluted things try that first.