Yes, you can use TurboTax, but depending upon the type of entity your business is will determine which TurboTax product to use.
If your business is a sole proprietor or a single member LLC, then you can use TurboTax Self Employed (online version) to file your business information on your personal tax return.
If your business is a multi-member LLC, partnership, S Corp, or C Corporation, you will need to file a separate return for the business which can be done using TurboTax Business. Your personal income tax return can then be prepared using one of the individual income tax products.
TurboTax Business (CD or download)