The cost of Bay Area Sportfishing boats...

Why do Bay Area Sportfishing boats seem to cost more than SoCal boats?

Maybe it's because of capacity. From checking today's fish count, most Bay Area boats went out with less than 20 anglers, while most SoCal boats (excluding the 6-pack charters) went out with 20-30 anglers, and even the boats with less than 20 anglers still have the capacity to carry a far greater amount.
https://www.sportfishingreport.com/dock_totals/boats.php

Cost is generally a reflection of the local conditions. Higher expenses, fewer customers leads to a higher break-even point cost per customer.
I don't miss the upward spiraling cost of, well, everything from living up there.

I have a hard time seeing $300 for a halibut trip in the bay.

Not unless it has an open bar...

I could be wrong but I think they are pricing themselves out of the market for many people.

$300 for a trip sounds very excessive. I follow a lot of the Bay Area charter to see what's biting but I'd rather get some live bait and relax at a pier, thats just me.