I feel kinda mean for saying this but...
Why do you hesitate to say it?
I think I shouldn't say this but...
In this context, I think it's better to be honest about your feelings. You shouldn't feel bad for speaking out your mind.
My boyfriend doesn't have a dick
I'm not sure I understand what you are saying, but so far, I don't think it is terribly mean for you to bring it up.  Are you saying that your boyfriend is a trans-male who was born in a female body, but does not identify with that sex?  Or do you think that he was born with very small genitalia?