The
Marquis of Hamilton (later Duke of Hamilton) has the strongest geneological claim (descent from James II of Scotland, making him the heir by proximity of blood or by male-preference primogeniture), and his grandfather had been James's official heir before James produced children of his own.
The
Duke of Lennox is another possibility. His line's claim came from being the senior surviving legitimate male-line branch of the Stuarts/Stewarts, although they descended from a pre-royal branch. There were times when the Lennoxes were in a stronger position to inherit than the Hamiltons (particularly around the time of the Gunpowder Plot, when the senior Hamilton heir was a confined lunatic and the runners-up were a young child and an outspoken Catholic respectively, while the Duke of Lennox was a senior member of James's government), but I don't know if this was one of those times.
The
Earl of Moray was also in the mix, being descended from Robert II of Scotland along a female line on his father's size, and from James V of Scotland along a bastard line on his mother's side. His claims were weaker than those the other two lines, so he's only be a serious contender if there were major political problems I'm not aware of with the other potential heirs.
Unless someone who knows a lot more about Scottish politics during this period than I do wants to correct me, I think Hamilton is the likely heir if Elizabeth and her children were for some reason to be skipped.