Fishing Charter - Do it in Cabo
I would recommend doing the day of fishing from Cabo - while I hear that there are now some charters running out of the marina in San Jose, I think you'll get a better deal in Cabo. Try Redrum - they are probably one of the best.
Another choice is to check out
www.loscabosguide.com and click on their discounts page. There should be a fishing charter company or two listed there with a 35% discount - just make sure that you can get the vouchers from the local office, not the California one. Or you can try
www.cabosanlucastours.net - they have some great discounts too - all you need to do is choose whichever one you want and print out your certificates.
As you probably already know the marina is full of sharks - timeshare sharks, deep sea fishing sharks, etc. I would strongly caution against choosing someone at random at the marina - lots of people have posted bad experiences on Trip Advisor when they go that route. You could also check out the Cabo Forum on Trip Advisor for fishing reports - all the reputable charters are listed there in various posts.