I would like to take a picture with my friends A and B
(only A and B in the picture,and I am a photographer)

In this situation, I should say to A'' Could you take a picture with B''
OR''Could I take a picture of you and B''
OR are there any better way to say more naturally?

Question

I would like to take a picture with my friends A and B
 (only A and B in the picture,and I am a photographer)

In this situation, I should say to A'' Could you take a picture with B''
OR''Could I take a picture of you and B''
OR are there any better way to say more naturally?

Answer

Can I / Shall I / Should I / Let me / Lets / Why don't I /  Why not let me / Is it ok if I  /.. Take a  photo / picture of you (two) together.

Actually in this situation English is extremely flexible.

If you say as you suggest " Could you take a picture with B''.. you are asking requesting that person A takes a picture with B and B is unknown. Unless you are suggesting A takes a selfie with B.

Answer

"Could I take a picture of you and B ?"   [your second version]     OR
"Could I take your picture with B?"

Answer

Shall I take a picture of you and B together?

Answer

I would suggest:

Could you stand next to B so that I can take a picture of the two of you?

Answer

>I would like to take a picture with my friends A and B
 >(only A and B in the picture,and I am a photographer)
must be
to take a picture _of_ my friends