Thanks for posting your question. I can tell that you are a very careful and thoughtful mother who is very sensitive to the importance of male role models in your son's life.  
 
There is no right or wrong, easy answer to your question. As you mentioned, because of your son's age, he won't be able to understand complicated explanations to his biological father's whereabouts, but I think that you can begin to explain things to him in a simple way at this point. Explain to him that, like all children, he does have a father who helped "create" him (whatever language you feel comfortable with), but for a number of reasons (remain vague), he is not available to live with the two of you. It is natural for people to want to spend time with a partner, and you have begun spending time with [boyfriend's name here]. Although he is not your son's daddy, he cares about your son very much, and he enjoys spending time with him. If you and your boyfriend are comfortable with your son calling him daddy, tell your son that he can do that because you understand why he would wish to have a daddy in his life.
 
As your son gets older, he will understand the nuances of the situation with greater clarity, and I would encourage you to always be honest with your son (of course, no need to tell him sordid details, if they exist, until he is in his tween or teen years). Secrets have a way of creating problems in families.  
 
Take care and best wishes.  
L. Compian, Ph.D.
Child Psychologist
Education.com