I am employed with a company and taxes are taken out of my weekly salary.

I also get a quarterly commission check and end of the year bonus.

Question
On my next commission check (coming July 2nd), can I "1099" that check so no taxes are taken out? The company I work for says that isn't allowed but a couple buddies of mine have done this in the recent past.

I am fully aware of claiming that income and paying the taxes.

In advance, thanks!

Generally no - either you are an employee (on a W2) or an independent contractor ; you can't be both for the same job. Also, keep in mind that if you are paid on a 1099 the amount of social security tax you will owe is double the amount that you pay as an employee on a W2. Why would you want to pay double social security?