You'll definitely want to stick with Nepali owned companies. All the westerner led trips are twice the money. I used Mountain River Adventures for a Tamur raft trip a couple years ago. They were good on the water and our guide Raju was very skilled. My wife and I managed to keep in the boat even during repeated dumptruck attempts however... So on the water they were great and Tej, the front man, was good a the communication part before and during. What they sucked at was transport logistics. This was doubly bad because that is why I hired them--I don't need help once on the water. We had three nights of arriving to some crossroads town well after normal people are asleep with zero planning for connections or lodging. The second night, at Bastantapur, the driver they hired blared the horn of his microbus for half an hour until a local brothel owner kicked his girls out and let us into the nastiest, stinkiest, most disgusting hovel I've ever spent a night. . .
Don't forget to do some trekking while you are over there it is really not to be missed and it's so damn easy and cheap.