Kayaks are available for hire in Kathmandu and Pokhara, although you'll be hard pushed to find a shop with a load of boats stuck outside, as you find with many of the trekking equipment shops.
Most reputable rafting operators will have a selection of kayaks at their boatyards or shop in both Kathmandu and Pokhara. A reasonable price to pay is US$10 per day, if you are paying to do a river or doing a kayak clinic boat hire will usually be included in the overall cost.
For longer periods most companies will be prepared to negociate a long term discounted rate.
But. . . . . . . .
There's only one specialist kayak hire shop in Nepal - Charley Ganesh's shop - take a look at Ganesh's link or click here.