Kinetic: The Certifications are granted by the US Sailing or ASA certified schools as you pass each level of training. You can also get certified by demonstrating your skills (without the training), joining the association & passing the written test(s) plus any local school requirements.
Some schools / clubs require you to become a member to charter their boats or to obtain their member (lower) charter rates.
In US Sailing, there are 5 levels from basic keelboat (entry) to Ocean Passagemaking. ASA has similar. The level you are certified for will usually determine what size/type boat you can charter.
Here in SF Bay, most of the charter operations are part of schools/clubs. Each has their own set of approaches, rules, charter fleet & styles including whether you have to be a member of that particular club to charter their boats. They are also spread around the bay which will provide different conditions in & around the school/club location (marina / proximity).
SF Bay is known as one of the most challenging (and lots of fun if you like wind) areas to sail considering the geography, commercial traffic, pleasure craft, currents in certain areas & summer winds.............so each charter operation will definitely make sure (or at least should) the skipper & crew are qualified.
The costs vary from school/club on training, chartering, membership (if necessary or on-water testing (if you feel you can pass without training). The sailing association fee is usually the same no matter what school/club you choose. It will include a Log Book to record your training level / certification & allow you to track your charters & other experience. There are also training materials produced by each association for each level.
Suggest You visit several schools/clubs to see their facilities, check out their boats, understand their approach/rules & get a feel for the staff/members.
this link should help identify resources in the bay area.
I went thru that process when I moved to the area 6 yrs ago & very happy @ OCSC in Berkeley.