If your father has essentially served as your supervisor and is the best one to comment on your strengths and abilities, then it is definitely appropriate for him to write one of your letters of recommendation. More than anything, admissions officers want to hear from someone who knows you well, and they know that people coming from a family business will be in a somewhat unique situation with regard to their letters of recommendation.
If you could only submit one recommendation with your application, then this would be a tough call, but most top school ask for two or three of them. Just make sure that, in addition to your father's recommendation, you provide at least one other letter from a work-related contact who knows you well. This could be a partner or a customer who has worked with you enough that they can provide specific examples of your strengths and achievements.
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