Fire and smoke conditions in any one place are impossible to predict a month in advance. Just keep in mind that even with all of the fires in the news, and as big as some of those fires are, California is huge so even with many fires it's very possible, maybe even likely, that they won't be affecting Yosemite at the time of your visit.
FAT is the closest airport but is smaller, so depending where you are coming from is more likely to involve a connection. I have visited YNP many times and usually fly in and out of SMF non-stop, I get to the park quicker than if I had taken the time to catch a connecting flight to FAT. SFO and other Bay area airports can be good but you are more likely to hit bad traffic driving to and back from the park. Another possibility is Reno if you enter the park from the east side.
The Top questions on the right will really help. Full TripAdvisor website
You have not included your home location, so specific advice about flights would be tough. I used SMF for many year, but now I can get inexpensive nonstop flights to FAT so that's my preference. There is a topic about airports in the Top Questions.
Definitely rent a car. No question.
To help planning your fall visit, check the topics about lodging, "when to visit", fall trip reports, maps, what to do in Yosemite Valley, what to do on Glacier Point Road, and what to do along Tioga Road.
Unfortunately, three nights is only two full days so you won't have time to enjoy all the 'best bits' of Yosemite. Research, plan, lay out a draft itinerary, ask for feedback here, and then head into Yosemite!
I am coming from Wisconsin. We were supposed to visit New Orleans but hurricane Ida caused that to be canceled. Looking for a replacement get away now. Perhaps I should wait to see Yosemite when I have more time?Edited: 16 September 2021, 22:39
Day 1: Fly into Fresno and drive to Wawona and explore. Continue to Lodging
Day 2: Explore Yosemite Valley
If you can’t get a flight that arrives before 3!pm and leaves after 3 pm, would recommend one extra night as staging.
I would fly into reno so you can see the gorgeous fall colors in the eastern sierras on your way to Yosemite.. the area is back open from the recent fires. be sure to see them as this is best of the best in the area in October.