both are decent, yardhouse is popular but definitely overpriced. i didn't think yardhouse was at the rim unless there is a new one. the only one i know of is at la cantera. there are a few bj's around now and they have decent brew for a reasonable price.
if you want good draft beer, freetail brewery is a good place to go as well as flying saucer, of course these places aren't at the rim. freetail is nearby though.
I will have to second the Freetails recommendation. BJ's is a joke! Their beer is plain at best with no imagination or inspiration put into the brewing process. I liken it to the Applebee's of the brewpub world. I've been three or four times now hoping that with some time the place would get better. no such luck.
As for the Flying Saucer, IMHO it used to be one of the best places in town to get a beer. Now every time I go in there it seems to be jammed full and staffed with waitresses with bad attitudes. About three years ago when I first started going there the wait staff was pleasant and reasonably knowledgeable about the beer they were peddling. It almost turned into Hooter's with a better beer selection.
They had a Belgian-style around New Years that was damn good too. Doesn't actually compare to any of the great, authentic Belgians (nothing does), but still, it was mighty tasty for an American-brewed Belgian-style. For comparison, think more along the lines of Allagash than Duvel.