There is no direct bus from Kathmandu to Muktinath or Pokhara to Muktinath. You have to change 3-4 buses/jeeps to reach Muktinath. You can only ride your bike up to Muktinath. Bus route for Muktinath will be Kathmandu-Pokhara-Beni-Tatopani-Ghasa-Marpha-Jomsom-Muktinath and back same route. Bus/jeep may charge somewhere between Rs. 400-700 per person.
There are few lodges/guest houses around the bus stops. You can separate Rs. 1,500-2,000 per day per person for Breakfast, lunch, and dinner.