Is it permissible for the contractor to take tools and equipment from the company to satisfy his right, which is being withheld from him, especially since he paid the workers' wages from his own money?

If you are certain that the company has wronged you and unlawfully withheld your rights, then it is permissible for you to take what is rightfully yours, without exceeding your due entitlement. This is known as "al-Zafar bi al-Haqq" (gaining one's right), provided that no harm befalls you as a result. We advise you to leave this company and seek another opportunity.