I am staying with him for a few weeks and I feel the need to go to confession but don’t feel comfortable going when he will know who I am. Is that a legitimate reason for not going to confession?
It’s a legitimate reason for not going to confession to your uncle. Just as doctors ordinarily don’t treat their own families, it is ordinarily preferable not to receive confession from a priest who is a family member (except, of course, in a case where the family-member priest is the only priest available and you are in danger of death). That doesn’t mean that you should avoid confession altogether. Let your uncle know that you need to go to confession and ask him to recommend another priest to whom you can confess.