It's hard to avoid the crowds in the main valley but the Half Dome Village is a convenient location right in the heart of the park. The accommodations there are heated tents on platforms with cots. The Majestic Yosemite hotel, also in the park, is more upscale and expensive if you want a bit more comfort.
There also a very popular and hard to reserve option for people wanting to camp with our carriyng all of their gear. A series of five camps form about a 50 mile loop in the high country off of the Tioga Road. Hikers stay in tents set up on platforms and are provided dinner and breakfast before picking up a lunch and hiking 8-10 miles to the next campsite. You have to reserve this far in advance.
Outside the park is the Tenaya Lodge which is a nice option if you don’t the mind extra driving time getting to the valley. Another option is the Rush Creek Lodge, also just outside the main part of the lodge.
A couple of restaurants if you need a bite on the way to the park are the historic Iron Door in Groveland and the 1960’s themed Sno White diner , for hamburgers and shakes in Oakdale.
The Whoa Nellie Deli located in the Mobil gas station is the place to stop in Lee Vining at the eastern entrance of the park.
The valley floor is beautiful and has lots of nice hiking/biking trails. Check out the climbers on El Capitan from the large meadow below it. Look for reflections of the mountains in the ponds early in the morning when the water is still and the crowds haven't taken over.
Heading up to Yosemite from Oakhurst is Alicia's Sugar Shack, a nice bakery in the town of Sugar Pine.
The Mist Trail is one I'd recommend. If you are up to it do the round trip that comes back down the John Muir trail.
Another must do is the Taft Point and Sentinel Dome hikes which can be done as a loop or individually, plus be sure to check out the view from Glacier Point (sunset is better for photos here or at night as seen below). There's a shuttle that you can take from the valley but you need to book it well in advance, or you can drive up there yourself. One hike I'd like to do on my next visit is from Glacier Point back to the valley floor via the Panorama trail. Since it is one way, taking the shuttle up is the way to go if you do this one.
On the way back from Glacier Point be sure to stop at Tunnel View which is the iconic view of the valley, best at sunset.
A drive along the Tioga Road is also worthwhile with stops at Olmstead Point, Tenaya Lake and Tuolumne Meadows. If you like climbing I the view from the top of Mt. Hoffman, above May Lake is worth the climb.
Also nearby is the trailhead to Upper Cathedral Lake one of the more scenic places in the park.
Check out this site, some good info on some of the best hikes to do while there, with detailed descriptions.