Hi,
If you want to do it based on the joomla user group of the user, you will need the Business edition of HikaShop which will allow you to define a user group restriction for your tax rules when you create them via the menu System>Taxes.
Otherwise, you can also manage that based on the user address ( with the company custom field turned on in the menu Display->Custom fields) with the "client type" field of your tax rules so that users specifying a company name in their address will be considered as a company and otherwise as an individual.