1. They're talking about revenue-share, not a share of units. That 91% revenue-share is very likely to translate into a somewhat smaller share of units because Apple's Mac ASP is probably substantially higher than the overall Windows ASP, even when you're restricting both to the $1000+ segment.
2. They're talking about PCs sold "at US retail". I'm not sure what their definition of that is (I couldn't easily find the original report), but there are two things it almost certainly does not include: sales to businesses and direct sales from manufacturer websites.
I find that unsurprising. I think it would be hard for NPD to gather that sort of data. However, both segments are important in $1000+ Windows PC market. Business buy plenty of $1000+ PCs (I'm sitting in a room of them). And the best price for a $1000+ consumer PC is almost always at the manufacturer website. I strongly suspect that, for most manufacturers (except Apple), the majority of $1000+ PCs are sold directly from their website.
Wait, what? Do you have a source for that? I'm pretty sure these numbers are not correct.