Hotel
If your looking to stay in Downtown San Diego we scored a great deal at the Courtyard Marriott right in the trendy Gaslamp district where all the restaurants and bars are. $99/night! Full disclosure this is not walking distance to the venue, but also not terribly far, so we would highly recommend utilizing a rideshare such as uber for the night.
Hotel
The Catamaran is walking distance to our venue, but alas we could not get a discounted rate for our wedding here :( It does have beautiful grounds, a great spa, and... location, but it is a bit pricey.