If you're into castles, then Castle Bolton is an absolute treat. Barden Tower may no longer be accessible, but is worth stopping off at. Skipton Castle is lovely, and well worth a visit.
Boat trips from Skipton up the Leeds-Liverpool (don't miss out the Springs Branch at Skipton!)
Short walk up between the Springs Branch of the canal and the mill race at Skipton (next to the Castle) is usually delightful
Grassington is lovely, with tearooms and plenty of short walks.
Settle-Carlisle is brilliant.
Malham Cove, yes, but also Gordale Scar adjacent. Kids love climbing up the waterfall and walking round to the Cove over the limestone pavement. There's a good climbers' cafe at Malham, and a big car park at the NP Visitor centre, but it can get very busy round Malham in summer. While you're up there, mind, go to Janet's Foss.
On the subject of waterfalls, head North to High Force and Aysgarth Falls. Beautiful, and really impressive, especially after the rain.
Hawes Creamery is especially good for Wallace & Gromit fans.
Kilnsey Crag is worth seeing, and Mastiles Lane, so long as it isn't completely destroyed by 4x4s now (it's a while since I've done it) is beautiful.
Bolton Abbey & The Strid - complete with stepping stones at the Abbey!
Steam trains from Embsay
Settle is a nice little town with lots of interesting little shops. And kids are bound to giggle at Ye Olde Naked Man cafe!
Skipton has some of the best chippies in the country, with Eastwoods supreme (or at least it used to be). But go to the Woolly Sheep on Sheep Street for great food.
I'll think of more stuff in a bit...