Is it permissible to take the money from selling empty computer printer ink cartridges, or does it belong to the company?

These empty containers belong to the company, and it is not permissible to dispose of them by selling or gifting them except with their permission. Since you have sold the containers and taken their price, it is obligatory to inform the company of that. If they permit you to take the amount and sell the containers, then that is well and good. Otherwise, you must give them the value of these containers and refrain from selling them in the future except with their permission.