I don't think anyone really can say where the queen is at. I've observed queens walking on the surface of the cluster, then disappearing into the clump of bees. I have always presumed her to be in the upper third of the cluster as this was what I was told by my mentors.
If I shake the cluster from a branch onto an inner cover of a brood box, I'll always try and watch for her entrance, which coincidentally comes toward the latter half of the swarm going into my swarm box. But I don't know if that tells me where she's at in the cluster. The cluster usually hits the top of the inner cover, cascades down all four sides, then reverses into the hole of the inner cover.
In cases where I cannot shake a branch, I've been more inclined to use a bee vacuum. You get all the bees, which I presume includes the queen though I don't see her, and vac's work great among small branches, concrete barriers, mail boxes, vining bushes, etc.
In conclusion, I take all the bees I can (to the relief of the homeowner), leave a few scout bees behind, and hope I get the queen. Time will soon tell, and with a bee vac, I almost always get the queen.
All the best,
Grant
Jackson, MO
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