First, it sounds like you have a small business, so you should first contact your attorney and accountant. They may advise you to contact the local police - this is theft, pure and simple.
Don't muck with your computers or other records - they may be evidence. You may need a computer forensic investigator to determine where the fraud was.
You should be able to review your own bank records to see where the transaction was and to what account (you probably won't be able to see who the recipient was). The review of your own records should help determine who initiated the theft on your end. If there was a wire transfer, a signature or other record of the authorizing individual and time of transaction should be available and provided by your bank in the course of business.
If the funds transfer was done out of your company, it is most likely done by an employee. Sadly, most theft is internal.
If it was not done internally, then you need to get aggressive with your bank - then they have a security problem. This is a different issue and your goal should be to get your funds back. This is probably less likely than an internal theft, however. Again, your lawyer and account are your best friends here.
Finally, if the amount was not too large, you may be best off in writing it off. Lawyers, accountants, and consultants are not cheap. If it was an internal theft (or that is what you suspect), you should review your internal controls to ensure that only proper people can move money around.
Good luck.
