What is the shaft height, if I may ask?
I've been tall boot shopping a lot lately. I have found some boots that are oh-so-close... by that I mean the fit in the calf is perfect and snug. However I also wind up with same effect as you, when trying to tuck skinny jeans into them. And I'm talking even with my skinniest skinnies. I've concluded it's not the skinnies. It's the boot. If the boot shaft was just a smidgen shorter - hitting at a wider place on the calf, rather than above the widest place -- then the skinnies would tuck better because the top of the boot would grab and hold the skinnies and keep them smoothly in place, so they don't bunch up at the knee.
It's hard to describe in words but let me try again: the boots I've found fit snuggly and perfectly in the widest part of my calf, as they should. But because they are a smidgen too tall, they appear to gape at the top. Because the boot is hitting not at my calf, but above it.
The reason I figured this out is because I tried on a pair of Frye boots (Dorado) that were just a tad too tall, but that had slouchy leather, slouchy enough that I could scrunch them down a bit, just enough that they'd hold tight at the calf, at my preferred/ideal height for tall boots. However, the boots would then ride back up again when I attempted to walk -- and lo and behold -- my skinnies would then scrunch up around the knees.