A quick google search showes a place called Lorillard Tobacco at 1270 Main St. Their web sites says they carry pipes, tobacco and accessories. There are several cigar shops and one cigar lounge.
A quick look in the Pipe Store Locator in the header at the top of the page shows two good stores in San Diego. Click on Ca and go to Liberty Tobacco and Racine & Laramie Tobacconist. Both are excellent.