I’ve had the same problem with my rear Shimano brake for a couple of months. The problem is intermittent but when it happens the vibrations go right through me. So much so that I have to release the brake slighty for the vibrations to stop. However as soon as I release, I can brake again with no problem.
I’ve cleaned the caliper, fitted new pads, bleed the brakes, aligned the caliper but this has made no difference. I’ve looked at the rear disc and it doesn’t appear to be warped but I’m now going to swap the discs around, to see it the problem transfers to the front (and is therefore disc related).
If this doesn’t solve it, I guess I may need to buy new brakes!