Do you know exactly why your manager objects to your stimming? I ask because I wonder if there might be a way to stim without it bothering your manager. So, my first suggestion would be to explain that it is related to your AS and then ask him or her what about the stimming is a problem.
If you can't come to any kind of agreement with your manager, I would suggest going to someone higher up in the chain of command. If you do that, include some information about AS that explains the need to stim.
I would try to resolve it in a non-confrontational way if possible. I fear that most NT have great difficulty understanding the need to stim and may tend to side with your manager, simply because they may wrongly see stimming as "unnecessary" and think you are just being difficult.
If all else fails, though, perhaps it might work to make it a legal/discrimination issue. If at all possible, I would seek the advice of a lawyer on that -- an attorney could advise you about the prospects for success if you argue that the boss is being discriminatory. (My personal opinion is that you have every right to stim if you need to and the rest of the world should educate themselves about it before they criticize -- but I suspect you already know that the world rarely works the way it SHOULD.)