Best (non-chain) Mexican in Center City?
The best taqueria style joint is Jose's at 10th & Buttonwood, but that is barely Center City and the neighborhood is terrible. But the food is fantastic. The only real Mexican place in CC I know of is Las Bugambilias at 2nd & South, which is also the edge of CC, but it's nice down there.
I have heard there is a place in the Bourse food court that is good. Apparently the Mexican consulate is in that building and they cater to them. But I have never been,
Upscale Mexican is easier, you have Lolita, Xochitl, Taquilas, and El Vez. Zochitl just got a new chef and menu I think tonight, so hard to say what it's like anymore. Lolita is the best out of that bunch IMO. It's BYOT (bring your own tequila), cash only, and does not take reservations. Welcome to Philadelphia :).
Dunno if you know the area but just a little ways out of CC there are plenty of authentic taquerias, mainly down in South Philly but also towards Kensington. Also what is probably the best upscale Mexican around right now is Distrito, in West Philly just off the Subway. It's worth the trip if you are into that kind of thing.
It's not a sit-down joint, but one of our weekly papers just named Savoy Mexican Grille (part of a grocery store) as the best place to get Mexican food outside of South Philly, and it's very much in center city (on 18th St. off of Spruce). Haven't been myself, but Yelp seems to like the tacos.
I second Distrito for something hip, trendy and exciting, but I wouldn't call it authentic. Our best authentic restaurants are in the Italian Market neighborhood, which is walking distance from center city. Favorites in that hood are Tacqueria La Veracruzana, Taquitos de Puebla (not the cleanest place, though), El Jarocho and La Lupe.
Before the chef switch, some people were thrilled about Xochitl; it might be worth betting on, if the location works for you.