On Labor Day weekend, Mission Bay will be insane, not to mention dangerous. If you're into decent riding, I'd recommend 6AM dawn patrol because after about 10:00 it will be packed with jetski's and people who don't know how to drive boats. My kids are 15 & 17 and I wouldn't pull them behind my boat on Mission Bay on a summer holiday weekend.
A better option would be Carlsbad Lagoon but I'm hot sure if you can launch your own boat there. You can rent pulls though. http://www.carlsbadlagoon.com/
Or third, try El Capitan reservoir about 25 minutes east of Mission Bay in Lakeside. It hasn't been very crowded lately although it will be blown out after 10:30 or so. If you're just out for a day on the water, this will be a much safer option than Mission Bay. http://www.sandiego.gov/water/recreation/elcap.shtml
Lastly, if it has to be saltwater, San Diego Bay would be better (less crowded than Mission Bay). Launch for free at Shelter Island Boat Ramp in Pt. Loma, http://www.sdboating.com/ramps.htm
, then travel south past Coronado and Downtown to near the Silver Strand & Glorietta Bay.