Three days, two of which are travel , to photograph Yosemite in summer is a tough row to hoe.
If one is flying their own plane, can arrange for a car, and touch down at one of the small municipal airports just outside the park, it could be a productive trip. Otherwise, almost all your time will be spent getting there. It is two and a half hours from Fresno to Yosemite Valley in good traffic. About four from the Bay Area. In summer, the routes to and through the park (two-lane highways) are busy.
If one has the ability, the most preferable option would be to land in Lee Vining adjacent to beautiful Mono Lake, followed by Groveland (say hi to Kevin) or Mariposa. Mariposa is the least desirable only because I would favor working in the high country because the waterfalls are puny this time of year and the roads congested as folks make the loop in their cars looking for parking, lunch and scenery. Unless you are obsessed with the icons of Yosemite Valley, you are better off up high where the air is cooler, there are fewer folks, and spring is just peaking. Mind you, I am speaking from the perspective of a color enthusiast.
Mariposa is a one-hour drive from Yosemite Valley, but over two hours to Tuolumne Meadows. It takes a little less time to get to the high country from Groveland, and about fifteen minutes from Lee Vining.
With the right light, anything in the park can be spectacular any time of year. But the best light in Yosemite Valley is typically from October through March. There is more colorful light, lower angle and less intense. One can easily work all day. But the high country, which does not feature the concentrated beauty of Yosemite Valley, is stunning as well and not accessible by auto except from late June through October, typically.
The exposed granite, twisted junipers, sparkling lakes, meadows spilling over with wildflowers (and mosquitoes) are compelling subjects, many of which just mean stepping out of a car at a turnout. But three days? I lived in Yosemite Valley for fourteen years and it just whet my appetite.
Give yourself some time for a proper visit where you can truly soak it in. If you want some ideas, go to www.yosemite.org and pick up a copy of Michael Frye's photographers guide to Yosemite. He worked hard to map out the most popular photo spots. Excellent book. Should cost twice what it does.
As for crowds, it can be busy, with most of the people concentrated in the seven square miles of Yosemite Valley around the parking lots, restaurants and overnight accommodations. David Brower used to say, "The number of people one encounters in Yosemite is proportional to the square of the distance one is from a parking lot and the cube of the elevation one gains." In short, get out of your car and you'll have a much more pleasant experience, even if it is just for a day.