The best way to broach this is to be honest and tell him that you have a hard time with accents - make it clear that you are not criticizing his way of speech or his accent in particular, but rather you have a difficult time with accents other than your own. This is important so that he knows you are not making fun but want to understand him more clearly.
Once you've established this, you should repeat phrases you are not sure of to be certain you understand (it is just as rude to nod along like you understand when you don't). You can ask him to repeat or speak slower - always putting the deficiency back on yourself.
Having lived in multiple parts of the US, with a wide range of accents, and traveled worldwide, I know that I can sometimes be hard to understand - set the expectation that they may need to be patient with you and you should be in good shape.