If you want to be on the water then a houseboat is your best bet. There are a number of places that rent houseboats, such as Herman & Helens, Paradise Point, Walnut Grove marina, etc.
As far as a cottages go the only place I have personally seen is B&W resort:
http://www.bandwresort.com/ I have been to the marina but have never been in any of the cottages so I can't comment on what they are really like. Look reasonable from the outside though.
Another place I know of but have never actually been to is Snug Harbor:
http://www.snugharbor.net/aboutsnugharbor.htm An online "cabin rental" place that has listings for all over is
http://www.vrbo.com/vacation-rentals/usa/california/central-valley/g#6510 They show two listings, one at Discovery Bay (would not be my favorite place for a week) and a place near Rio Vista that looks very interesting.
There are numerous places to camp. Tiki Lagun or Turner Cut near Stockton. Tower Park near Lodi. New Hope Landing in the north Delta area.
My overall favorite place to be is an area referred to as the Meadows, along Snodgrass Slough in the north delta (north of Walnut Grove). This is best experienced in a houseboat, which makes it a perfect destination if you rent a boat from Walnut Grove Marina.
Otherwise, just about any spot in the delta will give you reasonable places to ride. If you are going to be there for two weeks plan on touring the area. Definately take a trip to the Meadows (expect it to take all day). Buy a map and just cruise around! There are plenty of marinas scattered all over so you can stop and eat or refuel.
As for a local to give you pointers, there are lots available! A bit early to be making plans though.
Good luck, have fun!