Echo Mumblechums advice, especially re lunch time clubs.
At DS's school, because he had real problems, they made him a librarian, which meant he could have an early lunch pass and always had somewhere to go and do. This suited him, because he is an avid reader, and the school were able to justify it under the Gifted and Talented provision. (Only older children are eligible for appointment as librarians.) It worked really well. By y8, he is going to the library less and less, but for that first year it gave him a sanctuary and a group of people to belong to.
Don't delay speaking to the Head of Year, or whoever has responsibility for pastoral matters. Children's confidence, especially boys, can rapidly deteriorate, making the whole situation beyond them. It isn't - it is so easily solved. One school I know of has a jigsaw club, another has a science teacher who runs a lunch time board game club. They are essentially structured play environments, which sounds like it is just what your son needs. The chances are your son's school has something similar. Speak to the Head of Year and find out what they can do for your son. Transition to secondary is really hard, and unlike when we were children, most schools are switched on to this.
The best advice I ever got was from a Head of Sixth form (at a different school), who said, when I told her of our problems, 'Kids always think they can sort this stuff out themselves, and they never can. Speak to the Head of year and they'll sort it out.'
After a month of dilly dallying, I did go to the Head of Year and they did sort it out. I just wish I had done it sooner.
Very best of luck. But believe me, if you grasp the nettle now, the chances are you will be amazed at what the school can do for you.
(Also, in my experience, secondary schools are miles better at identifying and sorting out bullying.)