I'm going through the same questions you're having. I want my boat at the Delta so here's the info I've found:
This is kinda what I've found. Go to http://www.californiadelta.org/deltamarina.htm
and that will have most of the marinas on the delta w/ phone # or website. Rod is right about finding the place you like to ride and get a marina closest to there.
Discovery Bay is around $80 buck/mo to have your boat up on the racks...but they charge $ every time you launch...it is $20 per launch! but may be cheaper if you're boat is stored there..but i think it may be the same? Oh, and they close at 5 weekdays and 6 fri and sat. I think.
Orwood is also one of the closest...they are expesive...but you get a individual alarmed stall so you could leave all your gear in there and not haul it back and forth each time. but you do have to launch your own boat...so no driving up in the Honda..... They have a pretty long waiting list also... ~$150 if you have a foldable tower....more for the 14' doors.
Bethle Island has tons of marinas...I have a buddy that stores his at Russo's and it is around $110 i think. It is under an open sided boat shed thing....but they launch your boat for you.
That is about all the specifics I know. Hours of operation are key...as you'll have to have your boat back by the time they close or your boat will just sit in the water until the next morning when they can tack it out....and i'd be afraid they forget or something?
I'll probably have it figured out for me by the end of the month for sure..so feel free to email me in a week or 2 and i'll give you the low down on my place of choice. With the $ you save on launching and towing the boat back and forth i figure it is a small price to pay.......