After some further research and digging around in the database I was able to get the list of categories from the organization by using the following:
Organization organization = OrganizationLocalServiceUtil.getOrganization(companyId,usersExternalOrganizationName);
long organizationPK = organization.getPrimaryKey();
List<AssetCategory> assetCategoryList = AssetCategoryLocalServiceUtil.getCategories(Organization.class.getName(), organizationPK);
Hopefully this helps someone else in the same situation.
