Get your taxes done using TurboTax

If these are two unrelated businesses,  report them separately. In TurboTax,  I'd report the 1099-MISC on one of the Schedule C's, to make sure that the IRS sees that you reported it, rather than dividing it and reporting a portion on each Schedule C.

However, to accurately reflect the income from each activity, I'd deduct the portion of the 1099-MISC that relates to Business B from the amount reported in Business A as a miscellaneous expense on your Schedule C. Then report that amount as Other self-employed income on Business B. 

However, if these two businesses are closely related, you can report all of your income and expenses together on one Schedule C.