There are many, what in specific are you looking for? What is your budget?
Shechen guesthouse is pretty nice, but expansive. I think I payed like 7 Dollar a night. Padma Guesthouse is also nice, but really expansive, around 20 dollars a night, it is directly on the Stupa though.
Personally i would recommend you Dragon Guesthouse, it is behind Shechen and it looks very nice. I think it is cheaper, like around 300 Rupees a night. I havent seen the rooms, but people say it is nice and I can say that the food is pretty good. Next best is Lotos Guesthouse, also around 300 Rupees a night, but as far as I could see there are shared bathrooms, so you will not have your own one.
Every mentioned guesthouse is less than a 10 minute walk to the stupa. http://www.muktinath.org/travel/dragon.htm