Which is the only pyramid with a subsidiary burial place in it? - (Unless the queens chamber in the great pyramid was intended for some else)

Do you mean the Bent Pyramid? Sneferu MAY have been buried there, and the second chamber is thought to be the original burial-place of Queen Hetepheres.

It is later than the giza pyramids

Since no one knows or cares - Pyramid of Amenhet III (12th dyn) has a place for princess Senebtisi - who seems to be the 1st princess with a name in a cartouche.
She was actualy buried in an undisturbed but water damaged tomb quite nearby.
This information comes from my notes made in a dark lecture theatre a couple of months ago so appologies for any errors.

I thought you meant a burial with-in a pyramid.
Actually, there have been several subsiderary burials. The one that immediately comes to mind is the Pyramid of Khufu. There are three subsiderary pyramids in the enclosure. His mother, Hetepheres, whoes empty tomb was found in the area, was thought to originally have been buried in a subsiderary pyramid at the site of one of her husbands (Snefru) pyramids, the Bent. In fact, most pyramid enclosures had subsiderary burials, usually of the Pharaoh's wives.

I did say 'burial place' not an actual burial.