Will he sit on your knee to be stroked? My previous bun didn't really like being held but would sit on my knee to be stroked (for short periods), so I would clip her nails then - often just one paw a day.
Failing that, just be very firm. My Current Bun hates it too and he's a big, strong boy, so it's no fun when he fights. I can clip his claws on my knee now, but at first I used to put him on the kitchen table (which he wouldn't jump from as it was too high) and hold him there and go round his claws.
Persevere and clip them little and often so he gets used to it.