You must report the net income of the business on your tax return ($5000 from your example).
If the business is a single-member LLC, then the income and expenses are reported on Schedule C of your return; if there are other members/partners of the LLC, then you would report your share of the earnings from your Schedule K-1 of the business' tax return.
(The amounts you withdrew from the business account are not considered income - they are withdrawals or distributions).
