The simple answer to your question is this: When you are both in a good mood, raise the issue as calmly and kindly as you can. Tell him that you know he doesn’t mean anything by it but that it makes you and others uncomfortable. Not everyone likes to be touched in a familiar way. Ask him if he can please not touch people unless they ask for it or reciprocate.
However, what concerns me more than the incidents you describe is that you feel inhibited about talking with your boyfriend of three years about something that concerns you. You are both mature people in your 50s and you have been living together for some time. Why is it a problem to have a conversation with him about this? I may be reading more into this than is appropriate, I know. But if there are many issues that you can’t talk about, you and “John” have some work to do on your relationship. Giving and receiving feedback in a loving way is an important part of an intimate relationship. It’s what helps us grow as individuals and as partners. If that is lacking in your partnership, I hope you will consider some couples counseling to help you develop it.
I wish you well.