A 2.5 hour tour of Mission Bay in a kayak is even better on a full moon. And, if you go during the summer months, you will get a front seat viewing of the nightly fireworks that go off at Sea World right there over the bay. I did this a couple years ago with a small group of people and it was a lot of fun to experience Mission Bay from the water.
Mission Bay park is the largest man-made aquatic park in the country. Even if you aren't here during a full moon, night time kayaking the bay is both exciting and romantic.
Tip: Bring a flashlight and light wind jacket- it can get a little breezy sometimes on the water. I also recommend keeping a dry change of clothing for after your trip. The water is generally smooth, but you do get a little wet just from splashing the oars or riding the wake if a boat passes.