New update: Just spoke to the ranger at the Summit Ranger office in the Stanlislaus National Forest, in Pinecrest. That office is now open, at least virtually. You can get your permit online for Stanislaus National Forest traiheads HERE.
All issued electronically via the website.
Note that this is only for travel completely within the Stanislaus National Forest. if your trip takes into Yosemite, for example, you'll need to call the office and talk to them about it. That number is 209-459-9236
Toyabe Humboldt (Hoover Wilderness, east side) is now issuing wilderness permits via Recreation.gov. Try this link HERE. While it may be a pain to use that system, it has one advantage. If you are flexible in your dates, you can see how many permits have been issued for each trailhead, and can choose a date and trailhead with fewer hikers...at least as of the date you apply.