I stayed at Bunaken Seagarden Resort, a very nice and welcoming place with simple clean bungalows. The owner, Sonya, is friendly and helpful, she speaks good English. If you travel alone, it is a good place to meet other travellers (divers), because you have breakfast, lunch and dinner al together at a long table. The food is good (except for breakfast). This place costs for a single occupany bungalow 23 euros, that is including food, water, coffee and tea.
I dived at Living Colors, not a budget option but really good.