I suppose the first question would be why?
Have they been there long?
If the bees are happy in a hole very high in a tree, then unless the tree is going to be cut down, I think I would leave them to it.
The same goes for the bees in the wall.
As long as they are causing no damage or harm and are not a nuisance.
You can perform what is called a trap out, but it's late in the year for that as it can take weeks and there's no guarantee of success.
There are videos on line showing how to do it.
If the bees in the stone wall are a nuisance, then the only option is pesticide and to seal up all the holes so there's no chance of a swarm taking up residence next year.
Failing that, the least you can do next year would be to put out bait boxes, should they issue swarms.