Butcher in San Diego
I live in Poway, so I go to Bisher's and I always get good service, advice, and meat (yummy sausages!). I also like Iowa Meats (we got the best apple cinnamon pork kabobs there) for their meat AND various canned/jarred/boxed items. It's a fun shopping experience. They're also closer to you, if you're downtown now.
Before I found Bisher's, I'd get ribeyes from Costco or the Carmel Mtn Ralphs and they cooked up juicy and flavorful. Just in case you wanted an alternative to a local butcher.
A friend of ours has gotten all buddy-buddy with Mike's Choice Meats in Oceanside (again, quite a drive for you) and I have to say his all-beef dogs can't be beat.
I feel like the Whole Foods in La Jolla is bigger and better stocked than the Hillcrest one, but that may just be my opinion. Good food, though, and nice seafood.
Iowa Meat (Mission Gorge Rd)
Bristol Frams Market (UTC)
Jonathan's (La Jolla)
Major Market (Escondido)
Bisher's Meat (Poway)
WholeFoods (La Jolla, there is also one in Hillcrest but I never bought meat at that location)
It also depends what kind of cuts/quality you want.
Jimbos is pretty good for organic beside Wholefoods
There are several places for Mexican cuts
North Park Produce (Poway) for Middle East/Mediterrean meat