I have had the same question when i went to Nepal last year. It boils down to three options basically:
1) Meter taxi: The last option you would want to consider. Normally, they are not spacious enough if you have multiple luggages. You might even end up paying way more. The vehicles are not very comfy -- no a/c in most of them. For me, i have no time to bargain.
2) Airport taxi: They charge a predetermined rate. I used it when i flew domestic from Bharatpur to Kathmandu. Vehicles are better than meter taxis. When i asked if a/c could be turned on, the driver told me it would be additional charge. Also, i think they have surcharge in the evenings.
3) Travels and tours: Little bit pricier but very comfortable vehicles equipped with a/c. Spacious for luggages. I have used this service few times. I even requested to have my family picked up so that they could come to the airport prior to my arrival. They all were waiting for me at doors. Hassle free ride to home after a long flight. Courteous drivers. It is totally worth it. I recently found www.simrika.com and it looks like you can completely book online without having to call or email anyone in Nepal.
Hope this helps.
PS: Get some medical masks for your Nepal trip, especially if you are going to be in Ktm.
