Definitely Barona Creek; here's a list of your options:
Here's a list I've been meaning to compile; hope it helps.
Where to play in San Diego?
Resorts:
Barona Creek 619-387-7018
This is the must play course in the San Diego area. Just a 30 minute drive from downtown, Todd Eckenrode’s creation in Wildcat Canyon offers a thrill for every class of golfer. The course features strategic bunkering, scattered at different distances, through the wide fairways. Firm and fast conditions put a premium on attacking from the correct angles to the highly contoured greens. Hotel and Casino on site.
Torrey Pines (reservations) 619-570-1234
South: The host for the 2008 US Open is set up as a test of the modern game. Even from the white tees (6,880) this course plays long. Rees improved the 3 holes he moved to the canyon’s edge (3, 4&14) but 18 double plateau greens are a bit repetitive. Greens still need work to justify the $100-$125 rate
North: The proposed redesign has been postponed, here’s your chance to play what could be William Francis Bell’s best work. Better use of terrain, nicely contoured set of pushup greens, surely the more scenic of the two courses.
Golfers can show up as early as they want to line up for the morning’s first hour of tee times (cars line up in the parking lot on weekends, during the week you place your golf bag in line in front of the starters booth on the balcony); singles stand a decent chance of getting off through the waiting list in the afternoon.
Carlton Oaks 619-448-4500
This Perry Dye redesign has all the "dye-abolical” trademarks: waste areas, pot bunkers bulk headed water hazards and many greens that slope away in the back. At 7,225 75.2/146from the tips it’s definitely the second toughest layout in the County. Lots of fun from the blue or white tees though. Hotel on site.
La Costa 760-438-9111
Fans of Dick Wilson will enjoy the artistry of the bunkering on the original tournament course. The bad news is it has been split into the South, with 9 holes shoehorned in by Wilson and the North with its’ additional 9 holes on ample ground with good movement across the street, done by Joe Lee Unfortunately neither nines are a match for the original work. Sometimes the Resort will let the first group off the North actually play the tournament course, so long as they can beat the first group off the South to the back 9.
Warner Springs Ranch 760-782-4270
High desert course is both scenic and challenging. The remote atmosphere makes this course special; resort rooms have no TV or phones! Little over an hour from downtown but very close to Barona.
Municipal:
Coronado 619-435-3121
Jack Daray designed San Diego’s “Hidden Gem”, built on fill dredged from the harbor in the 50’s, it has 4 holes that play along Glorietta Bay, subtle doglegs test driving ability, the pushup greens punish poor iron play, wind is often a factor. At $25/day for everyone it’s the best deal in town.
Balboa Park (reservations) 619-570-1234
Built in 1918 by William Park Bell, this short (6,281) trip out through the canyons and back across the mesa has remained a tough track to score on. Sam Snead’s course record 60, shot here while in the Navy in WWII, still stands. Views of downtown and the Coronado Islands, walkups should have no trouble playing here.
CCFAD’s:
Maderas CC 858-451-8100
Built on a hilly site this course promises the thrilling downhill holes off the bat, the key here is how much fun the uphill holes are. Neal Meagher’s perfect mix off unique green sites are worth the price of admission alone. Soon to go private when enough memberships are sold.
Del Mar National 858-792-6200
The only Fazio course in San Diego County; All golfers really want is a thrill; this course comes up short here. Very playable and takes a great picture, but the tea cups at Disney Land are more exciting than this place.
Privates:
Rancho Santa Fe CC
Don’t pass up an opportunity to play here. Max Behr’s 1929 layout got the highest Doak rating in San Diego County (5).
La Jolla CC
Canyon golf at its best from William Park Bell, built in 1927.
San Diego CC
Another William Park Bell layout with several barrancas was built in 1921. The redesigned greens seem unsympathetic to the Bell style.
Tijuana CC
The course claims a MacKenzie heritage, but it sure looks like a William Park Bell to me; possibly during his relationship with Tillinghast. Close enough to the border to take the trolley down and hop in a cab for the short journey to the golf course; public access allowed.
Pauma Valley
The only Robert Trent Jones course in San Diego County is in the high desert just past Barona; once rated within the top 20 in Ca.
Military:
Marine Memorial GC, Camp Pendleton 760-725-4704
Set within the expansive Marine base this course by William Francis Bell occupies a peaceful and secluded river valley 50 minutes from downtown. Somewhat shaggy conditioning here doesn’t detract from the enjoyment.
Miramar, Memorial GC 858-577-4155
Jack Daray shows how to turn a flat parcel of land into an interesting golf course at the old Top Gun base. Now a Marine Corp Air Station it has some of the best conditioned greens in the County; wind and FA-18’s are always a factor here.