Do you want to go down the River to San Francisco, or just stay in the Delta, and enjoy some of its beauty? Do you want a round trip--not repeating, or are you OK with taking some of the same route coming and going?
If staying in the Delta, try and make a loop to include some of the areas in both the Sacramento and the San Joaquin rivers.
I would pick up Hal Schell's Delta Map and Guide ASAP, and also a book on cruising the delta. Schell died in 2005, and his last book is 1995 if you can get a copy worth while, but not a lot of changes…since. --all of the ones I have are way out of date (not even sure that Schell's map is available, if not there is the Delta Guide by Franco. If you have the Garmin Blue Chart Mobile and Active Captain together they give some reviews on the various anchorages and marinas--plus it all is free (as I recollect). Be sure and update Active Captain before you leave home on WiFi. (which I just did and was disappointed that there were not many current reviews as I would expect) The Navionics electronic chart app is a bit better--but not that much better, than if I didn't have it, that I would buy it.
There is some good information at:
http://www.trawlerforum.com/forums/s28/ ... -6139.html
The ramp and parking is secure at the marina just South of Rio Vista where the Delta Cruise starts--Delta Marina Yacht Harbor. Another place where I have launched is at The Towers Marina and RV park closer to the freeway near Lodi.
If you want to stay in the Delta, I stayed at anchor, each night, rather than a marina.--often bow to the bank.
See
http://deltaboating.com/marinas-wdelta.htm (There is also a section on the bridges and restaurants, click on those). Check out the eateries on one of the sites such as Yelp or Urban spoon--and Active Captain for Marina reports.
My favorites are Locke Slough, the Meadows, Potato Slough, Steamboat Slough, etc. Marinas I have enjoyed include the Delta Marina Yacht Harbor (decent restaurant.) Herman and Helens (Delta type of hangout food). Hidden Harbor,( we spent a week there with friends in our sailboat--I think they take transients)
There are connections between the Sacramento River

Rio Vista, Walnut Grove) and the San Joaquin River (leading to Stockton) thru 3 mile slough. The Cross Delta Canal is only open at limited times, and there is an 8'4" bridge clearance at low water, I would not consider this as a reliable crossing between the river systems. There are several other major rivers: the American River, and the Mokelumne River. The Mokelumne is one of the major waterways up to Locke Slough and the Meadows on the back side of the Sacramento river.
There are a maze of Islands, Tracts and cuts. A few of these cuts have bridges which have limited clearance of 12'4" to 14"--if you can get under these, you are good--but you need to know the bridge hours (see Active Captain and the link to Delta Boating above). I suspect that some of our residents in this part of the world could give you a better concise tour for the limited time.
If you want to head down to San Francisco--there are marinas we have stayed at in Benicia, You can stop at marinas in Vellejo and go up the Napa River, or go up the Petaluma River to the municipal docks (where the Delta cruise goes), but beware of the bridge openings: You may have to call ahead for the Bridge in Petaluma.
Down the bay to Angel Island (moorings for overnight--docks only during the day I believe). Sausalito Schoonmaker Point Marina is a great destination--fuel dock up the way about a mile.
Pier 39 or South Beach in San Francisco. Jack London Square Marina , Oakland, and then back up the River to Rio Vista…more places than days.