They say cats like being alone. This isn’t completely true. We often want to be near humans, even if we’re not actually close with the people we live with. Your cat can be close to you, but may not be very close with you. Most cats do like their humans.
“Near” refers to distance, always. My water dish is near my food dish.
“Close” can mean physical distance or emotional/mental distance. “I’m close to my favorite chair” means that the distance from me to my favorite chair is very small. It’s near.
“Are you close with your assistant?” Yes, I like my assistant, and we are good friends, so, yes, I’m close with her.