12 years later, lol.
Anyway, seeing that you live in US, São Paulo is not a safe place, but it's not a warzone. Just be mindful of your cell phone, jewelry, etc. Santa Ifigênia is an even less safe place and, honestly, you won't find anything interesting there. It's a packed, shopping area for Brazilians because we don't have access to a big variety of stores like you do in US (not only big chains but also retrograming stores). You won't find much NeoGeo stuff there and, whatever you find, will be overpriced (even for you, bringing dollars from US). The NeoGeo scene was big in Brazil decades ago but that's thanks to bootleg MVS carts, not necessarily legit products. Most of the places that still have arcades are dirty, sketchy, and the machines are just poorly maintained (expect crappy sticks, broken buttons, etc.). Sorry to destroy your expectations.
In São Paulo you should enjoy the food, the parties, [some of] the people. Not NeoGeo. By the way I'm Brazilian but moved to Canada in 2016 in case you are wondering if you should listen to me.